MIDTERM_VICTOR_LEON
Victor Leon
11/2/2021
Meiosis is a specialized type of cell division where the genome is first duplicated followed by chromosome segregation which permits the generation of gametes with a different genome from the parents due to recombination. This dynamic process will require dramatic chromosomal dynamics, which could accumulate errors and result in aneuploidy and/or empty gametes. In mammalians, one method to identify proper meiotic cell division is by histological analysis by assaying the gonads anatomical structures and peruse for physical anomalies.
In Payseur et al 2018, they are interested about hybrid sterility and what is the mechanism behind generating high rates of aneuploidy and defects in the germ cells. They utilized mus musculus with the subspecies mus domesticus, They have analyzed the cellular types in the gonads to identify pathological traits in the cellular components in the gonads such as tubules, spermatogonia, meiotic cells and spermatids.
LOADING AND OBSERVING DATA
rm(list=ls())
setwd("/Users/victorleon/Desktop/biostats")
Pays <- read.csv("Payseur_data.csv")
# I want to check how many geneotypes are in our mice
Genotype <- unique(Pays$Class)
Genotype## [1] "" "PWD" "PWDXWSB F1" "MF2 WSB/PWD" "MF2 PWD/WSB"
## [6] "WSBXPWD F1" "WSB"length(Genotype)## [1] 7# Even thouth it says that we have 7 genotypes, there is only 6, since its counting
# an empty spacePARSING DATA
The F2 is the data of interest, since we suspect that these are the offspring having sterility defects and compared that information to the wild-type and F1.
# some of the columns are defined as characters instead of numeric
# Therefore, I had to change the nature of the data in some columns
# that I desire to analyze.
Pays$RelRTestiswt <- as.numeric(Pays$RelRTestiswt)## Warning: NAs introduced by coercionPays$RTestisWt <- as.numeric(Pays$RTestisWt)## Warning: NAs introduced by coercionPays$SpermDensity <- as.numeric(Pays$SpermDensity)## Warning: NAs introduced by coercionPays$MNSyncytiaPerTestis <- as.numeric(Pays$MNSyncytiaPerTestis)
Pays$VIIPachyperSertoli <- as.numeric(Pays$VIIPachyperSertoli)
Pays$VIIpachys <- as.numeric(Pays$VIIpachys)
# I subset the mouse in Parentals, F1 and F2
Parentals <- Pays[which(Pays$Class == 'PWD' | Pays$Class == 'WSB'),]
F1 <- Pays[which(Pays$Class == 'WSBXPWD F11' | Pays$Class == 'PWDXWSB F1'),]
F2 <- Pays[which(Pays$Class == 'MF2 WSB/PWD' | Pays$Class =='MF2 PWD/WSB'),]
# I want to observe how the data looks like, therefore I will make
# histograms and observe by eye if the parentals data is as distributed as
# the F1 and F2 generation.
# For example the first evident step is to observe the whole organ in this mouse
# and I would like to see if there is a skew.
hist(Parentals$RelRTestiswt, col= 'lightblue')
hist(F2$RelRTestiswt, col = 'purple')
hist(F1$RelRTestiswt, col= 'red', add= TRUE)
#Apparently the F2 offspring have a more distributed right testis weight vs adjusted
#body weight
# One good explanation is that the Parentals and F1 generation have small sample size,
# this is very problematic since it will biased the result, we would need to normalize the data
# to do a valid comparison.
summary(Parentals)## id Class RelRTestiswt RTestisWt
## Min. : 258.0 Length:12 Min. :3.096 Min. :51.70
## 1st Qu.: 623.8 Class :character 1st Qu.:3.551 1st Qu.:55.30
## Median :1250.0 Mode :character Median :3.840 Median :61.05
## Mean :1091.1 Mean :3.836 Mean :61.14
## 3rd Qu.:1425.2 3rd Qu.:4.042 3rd Qu.:66.33
## Max. :1526.0 Max. :4.503 Max. :69.90
##
## SpermDensity TestisWidth TestisHeight MNSyncytiaPerTestis
## Min. : 1.533 Min. :0.002574 Min. :0.002126 Min. :0.000
## 1st Qu.: 8.611 1st Qu.:0.003211 1st Qu.:0.002558 1st Qu.:0.000
## Median : 8.905 Median :0.003286 Median :0.002646 Median :1.000
## Mean :10.052 Mean :0.003251 Mean :0.002677 Mean :1.583
## 3rd Qu.:11.666 3rd Qu.:0.003387 3rd Qu.:0.002846 3rd Qu.:1.500
## Max. :20.000 Max. :0.003550 Max. :0.003094 Max. :7.000
##
## TubuleswApop ApopGonia ApopMeiotic ApopRS VIIsertolis
## Min. :0.0000 Min. :0 Min. :0.0000 Min. :0 Min. : 9.00
## 1st Qu.:0.0000 1st Qu.:0 1st Qu.:0.0000 1st Qu.:0 1st Qu.:11.00
## Median :0.0000 Median :0 Median :0.0000 Median :0 Median :13.00
## Mean :0.1667 Mean :0 Mean :0.1667 Mean :0 Mean :13.08
## 3rd Qu.:0.0000 3rd Qu.:0 3rd Qu.:0.0000 3rd Qu.:0 3rd Qu.:14.25
## Max. :1.0000 Max. :0 Max. :1.0000 Max. :0 Max. :20.00
##
## VIIpachys VIIRSs VIIPachyperSertoli VIIRSperSertoli
## Min. :33.00 Min. :111.0 Min. :1.650 Min. :10.14
## 1st Qu.:48.75 1st Qu.:140.8 1st Qu.:4.214 1st Qu.:11.04
## Median :59.00 Median :154.5 Median :4.823 Median :11.89
## Mean :57.17 Mean :158.3 Mean :4.552 Mean :12.24
## 3rd Qu.:63.75 3rd Qu.:161.0 3rd Qu.:5.120 3rd Qu.:13.19
## Max. :75.00 Max. :245.0 Max. :6.000 Max. :15.56
##
## VIIRSperPachy VIITubuleArea id.1 NES15816487
## Min. :1.985 Min. :34359 Min. : NA Length:12
## 1st Qu.:2.311 1st Qu.:43521 1st Qu.: NA Class :character
## Median :2.474 Median :44347 Median : NA Mode :character
## Mean :2.972 Mean :44938 Mean :NaN
## 3rd Qu.:2.983 3rd Qu.:48570 3rd Qu.: NA
## Max. :7.424 Max. :54194 Max. : NA
## NA's :1 NA's :12
## NES14294417 NES11134751 NES14286696 NES11074105
## Length:12 Length:12 Length:12 Length:12
## Class :character Class :character Class :character Class :character
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## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
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##
##
##
## NES09776162 NES09751386 NES11023996 NES11153066
## Length:12 Length:12 Length:12 Length:12
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11151676
## Length:12
## Class :character
## Mode :character
##
##
##
## summary(F1)## id Class RelRTestiswt RTestisWt
## Min. : 323.0 Length:6 Min. :2.452 Min. :39.20
## 1st Qu.: 618.8 Class :character 1st Qu.:2.533 1st Qu.:45.77
## Median : 843.0 Mode :character Median :2.586 Median :47.70
## Mean : 846.5 Mean :2.636 Mean :48.47
## 3rd Qu.:1125.8 3rd Qu.:2.599 3rd Qu.:52.55
## Max. :1306.0 Max. :3.074 Max. :56.90
##
## SpermDensity TestisWidth TestisHeight MNSyncytiaPerTestis
## Min. :0.5330 Min. :0.002827 Min. :0.001839 Min. :14.0
## 1st Qu.:0.5747 1st Qu.:0.003001 1st Qu.:0.002313 1st Qu.:28.0
## Median :0.7165 Median :0.003231 Median :0.002675 Median :32.0
## Mean :1.5222 Mean :0.003194 Mean :0.002527 Mean :29.5
## 3rd Qu.:1.1335 3rd Qu.:0.003341 3rd Qu.:0.002761 3rd Qu.:34.5
## Max. :5.3670 Max. :0.003575 Max. :0.002991 Max. :37.0
##
## TubuleswApop ApopGonia ApopMeiotic ApopRS VIIsertolis
## Min. :17.0 Min. :0 Min. : NA Min. : NA Min. : 9.0
## 1st Qu.:22.0 1st Qu.:0 1st Qu.: NA 1st Qu.: NA 1st Qu.:12.0
## Median :25.0 Median :0 Median : NA Median : NA Median :14.0
## Mean :26.8 Mean :0 Mean :NaN Mean :NaN Mean :13.6
## 3rd Qu.:31.0 3rd Qu.:0 3rd Qu.: NA 3rd Qu.: NA 3rd Qu.:16.0
## Max. :39.0 Max. :0 Max. : NA Max. : NA Max. :17.0
## NA's :1 NA's :6 NA's :6 NA's :1
## VIIpachys VIIRSs VIIPachyperSertoli VIIRSperSertoli
## Min. :32.0 Min. : 8.0 Min. :1.882 Min. :0.5714
## 1st Qu.:33.0 1st Qu.:31.0 1st Qu.:2.062 1st Qu.:1.8235
## Median :35.0 Median :54.0 Median :2.857 Median :4.0625
## Mean :36.6 Mean :43.8 Mean :2.899 Mean :3.5082
## 3rd Qu.:40.0 3rd Qu.:61.0 3rd Qu.:2.917 3rd Qu.:5.0833
## Max. :43.0 Max. :65.0 Max. :4.778 Max. :6.0000
## NA's :1 NA's :1 NA's :1 NA's :1
## VIIRSperPachy VIITubuleArea id.1 NES15816487
## Min. :0.2000 Min. :26850 Min. : NA Length:6
## 1st Qu.:0.9688 1st Qu.:27704 1st Qu.: NA Class :character
## Median :1.2558 Median :28558 Median : NA Mode :character
## Mean :1.2274 Mean :28328 Mean :NaN
## 3rd Qu.:1.7429 3rd Qu.:29068 3rd Qu.: NA
## Max. :1.9697 Max. :29577 Max. : NA
## NA's :1 NA's :3 NA's :6
## NES14294417 NES11134751 NES14286696 NES11074105
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
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## NES13812901 NES14871408 NES10364112 NES11685779
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES13788802 NES14853940 NES11672440 NES11892856
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14795958 NES11922718 NES13717684 NES16166231
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11844486 NES13983246 NES16140479 NES16125013
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14928053 NES11623637 NES14121839 NES11578614
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14962103 NES16324210 NES14090103 NES14075733
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES16294771 NES16273123 NES11443497 NES14999618
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11180909 NES11337944 NES16235275 NES16226083
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES16739796 NES16746959 NES16744861 NES14013407
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11310845 NES14253823 NES15042825 NES11289731
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14238702 NES15058121 NES16852927 NES11983479
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14187185 NES16893219 NES16884786 NES14174531
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11950844 NES11255058 NES14143018 NES08501092
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES08390448 NES08368561 NES08350023 NES08331256
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES08426982 NES08429161 NES08470326 NES08577121
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES08552323 NES08540153 NES08520186 NES15356530
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES15364695 NES17562029 NES17574394 NES11230998
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11225251 NES14390116 NES17617698 NES17671922
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES15514768 NES11367273 NES17700753 NES12438187
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES17761635 NES15486525 NES17098777 NES12472925
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14311136 NES17231622 NES12528524 NES12530308
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12580917 NES17301651 NES12644423 NES12652868
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12054881 NES17019164 NES17018369 NES12055753
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14550999 NES15688472 NES15709218 NES16491343
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES16519953 NES16533743 NES16533235 NES16568527
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES16574315 NES15074269 NES15202108 NES17371978
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES17415383 NES15800630 NES12684228 NES12723981
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12727989 NES12757042 NES15157241 NES13425967
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES13690842 NES15810853 NES13668382 NES17464901
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES13645394 NES13637114 NES13626096 NES13534761
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES13486940 NES10981276 NES10981283 NES17499105
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES17501358 NES10974496 NES10947357 NES12384176
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES09704766 NES09698120 NES09680036 NES09680385
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES09660234 NES09670667 NES09767342 NES09760621
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES09776162 NES09751386 NES11023996 NES11153066
## Length:6 Length:6 Length:6 Length:6
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11151676
## Length:6
## Class :character
## Mode :character
##
##
##
## summary(F2)## id Class RelRTestiswt RTestisWt
## Min. : 332.0 Length:312 Min. :1.462 Min. : 19.30
## 1st Qu.: 672.8 Class :character 1st Qu.:3.421 1st Qu.: 61.85
## Median : 971.5 Mode :character Median :4.222 Median : 75.95
## Mean :1050.1 Mean :4.212 Mean : 75.78
## 3rd Qu.:1482.2 3rd Qu.:4.946 3rd Qu.: 90.58
## Max. :1789.0 Max. :7.740 Max. :131.30
## NA's :2 NA's :2
## SpermDensity TestisWidth TestisHeight MNSyncytiaPerTestis
## Min. : 0.03333 Min. :0.002470 Min. :0.001966 Min. : 0.000
## 1st Qu.: 7.22222 1st Qu.:0.003215 1st Qu.:0.002902 1st Qu.: 0.000
## Median :11.38889 Median :0.003505 Median :0.003174 Median : 0.000
## Mean :12.18470 Mean :0.003518 Mean :0.003192 Mean : 3.453
## 3rd Qu.:16.86111 3rd Qu.:0.003805 3rd Qu.:0.003498 3rd Qu.: 2.000
## Max. :53.88889 Max. :0.004589 Max. :0.006860 Max. :224.000
## NA's :2 NA's :7 NA's :7 NA's :5
## TubuleswApop ApopGonia ApopMeiotic ApopRS
## Min. : 0.0000 Min. :0.000000 Min. : 0.0000 Min. :0.00
## 1st Qu.: 0.0000 1st Qu.:0.000000 1st Qu.: 0.0000 1st Qu.:0.00
## Median : 0.0000 Median :0.000000 Median : 0.0000 Median :0.00
## Mean : 0.9837 Mean :0.006515 Mean : 0.5407 Mean :0.43
## 3rd Qu.: 1.0000 3rd Qu.:0.000000 3rd Qu.: 1.0000 3rd Qu.:0.00
## Max. :13.0000 Max. :1.000000 Max. :11.0000 Max. :8.00
## NA's :5 NA's :5 NA's :5 NA's :5
## VIIsertolis VIIpachys VIIRSs VIIPachyperSertoli
## Min. : 8.00 Min. : 0.00 Min. : 28.0 Min. :0.000
## 1st Qu.:13.00 1st Qu.: 45.00 1st Qu.:114.5 1st Qu.:3.000
## Median :15.00 Median : 54.00 Median :138.0 Median :3.611
## Mean :15.13 Mean : 53.67 Mean :137.2 Mean :3.662
## 3rd Qu.:17.00 3rd Qu.: 62.00 3rd Qu.:161.0 3rd Qu.:4.310
## Max. :26.00 Max. :102.00 Max. :249.0 Max. :7.000
## NA's :13 NA's :13 NA's :13 NA's :13
## VIIRSperSertoli VIIRSperPachy VIITubuleArea id.1
## Min. : 1.120 Min. : 0.500 Min. :24334 Min. : 332.0
## 1st Qu.: 7.534 1st Qu.: 2.250 1st Qu.:38394 1st Qu.: 673.2
## Median : 9.562 Median : 2.547 Median :42638 Median : 971.5
## Mean : 9.426 Mean : 2.702 Mean :43223 Mean :1049.8
## 3rd Qu.:11.268 3rd Qu.: 2.964 3rd Qu.:47967 3rd Qu.:1481.8
## Max. :17.500 Max. :16.286 Max. :66328 Max. :1789.0
## NA's :13 NA's :14 NA's :48 NA's :2
## NES15816487 NES14294417 NES11134751 NES14286696
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11074105 NES12949347 NES12946173 NES14502456
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14483536 NES16480214 NES16491767 NES13067559
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12813781 NES12898360 NES08757020 NES08728879
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES09347685 NES09307918 NES09250843 NES09108608
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES09049532 NES08957389 NES08939262 NES08899242
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES08875111 NES08692489 NES12893054 NES10840465
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES10803066 NES10764269 NES15918417 NES10748871
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES13927401 NES10718395 NES10869248 NES10873191
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES16591962 NES10330741 NES10326824 NES08641863
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES08635080 NES09479212 NES09448372 NES09447649
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES09414902 NES09384272 NES09565397 NES09556388
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES09515784 NES09199844 NES09167199 NES10930789
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES10987252 NES10317794 NES10287075 NES10252883
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES10443817 NES16698285 NES16597883 NES10390397
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14691741 NES13812901 NES14871408 NES10364112
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11685779 NES13788802 NES14853940 NES11672440
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11892856 NES14795958 NES11922718 NES13717684
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES16166231 NES11844486 NES13983246 NES16140479
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES16125013 NES14928053 NES11623637 NES14121839
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11578614 NES14962103 NES16324210 NES14090103
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14075733 NES16294771 NES16273123 NES11443497
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14999618 NES11180909 NES11337944 NES16235275
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES16226083 NES16739796 NES16746959 NES16744861
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14013407 NES11310845 NES14253823 NES15042825
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11289731 NES14238702 NES15058121 NES16852927
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11983479 NES14187185 NES16893219 NES16884786
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES14174531 NES11950844 NES11255058 NES14143018
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES08501092 NES08390448 NES08368561 NES08350023
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES08331256 NES08426982 NES08429161 NES08470326
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES08577121 NES08552323 NES08540153 NES08520186
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES15356530 NES15364695 NES17562029 NES17574394
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11230998 NES11225251 NES14390116 NES17617698
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES17671922 NES15514768 NES11367273 NES17700753
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12438187 NES17761635 NES15486525 NES17098777
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12472925 NES14311136 NES17231622 NES12528524
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12530308 NES12580917 NES17301651 NES12644423
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12652868 NES12054881 NES17019164 NES17018369
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12055753 NES14550999 NES15688472 NES15709218
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES16491343 NES16519953 NES16533743 NES16533235
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES16568527 NES16574315 NES15074269 NES15202108
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES17371978 NES17415383 NES15800630 NES12684228
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12723981 NES12727989 NES12757042 NES15157241
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES13425967 NES13690842 NES15810853 NES13668382
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES17464901 NES13645394 NES13637114 NES13626096
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES13534761 NES13486940 NES10981276 NES10981283
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES17499105 NES17501358 NES10974496 NES10947357
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES12384176 NES09704766 NES09698120 NES09680036
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES09680385 NES09660234 NES09670667 NES09767342
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES09760621 NES09776162 NES09751386 NES11023996
## Length:312 Length:312 Length:312 Length:312
## Class :character Class :character Class :character Class :character
## Mode :character Mode :character Mode :character Mode :character
##
##
##
##
## NES11153066 NES11151676
## Length:312 Length:312
## Class :character Class :character
## Mode :character Mode :character
##
##
##
## # The statistics look better on the F2 generation definitely because of the data.
# To make a visual sense on the abundance difference I will plot the data.
par(mfrow=c(1,3))
plot(Parentals$TestisWidth, col= 'blue')
plot(F1$TestisWidth, col='orange')
plot(F2$TestisWidth, col='red')
# We can observe that there is a LARGE difference in data, therefore, inferring
#definite results will be difficult due to the sample size as I mentioned above, unless
#we generate information based on the data we have
par(mfrow=c(1,3))
plot(Parentals$RTestisWt, col= 'blue')
plot(F1$RTestisWt, col='orange')
plot(F2$RTestisWt, col='red')
# As a simple examples we can compare the means and see if there is any difference in variance
# and average.
mean(Parentals$RelRTestiswt, na.rm = T)## [1] 3.836167mean(F1$RelRTestiswt, na.rm =T)## [1] 2.636mean(F2$RelRTestiswt, na.rm = T)## [1] 4.211551# We can see here that the F2 has a higher average compared to Parentals and F1
sd(Parentals$RelRTestiswt, na.rm =T)## [1] 0.426402sd(F1$RelRTestiswt, na.rm = T)## [1] 0.2218134sd(F2$RelRTestiswt, na.rm =T)## [1] 1.170696# We can see here that the F2 has a hhigher standard deviation, which is also
# reflecting the higher variance, in this case this is not pf much help because of the
#sample size
mean(Parentals$SpermDensity, na.rm = T)## [1] 10.05183mean(F1$SpermDensity, na.rm = T)## [1] 1.522167mean(F2$SpermDensity, na.rm=T)## [1] 12.1847# The same for sperm density. All of this data indicates that F2 will have particular phenontypes compared to parentals and F1 generation.
In conclusion, it will be difficult to compare the F2 to the F1 and Parents since the sample size differs. I would randomly choose values from F2 and equalize the amount of data in the Parental and F1, and so on. Once I have covered at least all the possible values of the F2 then, this data would support a solid paper.