Maris_2013_Table_1

library(Biobase)

## Loading required package: BiocGenerics

## Loading required package: parallel

## 
## Attaching package: 'BiocGenerics'

## The following objects are masked from 'package:parallel':
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## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.

library(GEOquery)

## Setting options('download.file.method.GEOquery'='auto')

## Setting options('GEOquery.inmemory.gpl'=FALSE)

#Author: Abigail E. Moore

#This code reproduces the CIT discovery dataset info from Table 1 of the following source:
#Marisa, L., Reyniès, A. D., Duval, A., Selves, J., Gaub, M. P., Vescovo, L., . . . Boige, V. (2013). 
#Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic Value. 
#PLoS Medicine, 10(5). doi:10.1371/journal.pmed.1001453

#GSM 971957:972399 are the discovery dataset
#GSM 9772293 is marked "NA" for age


###Loop through .soft files to get the necessary data for this analysis into a dataframe

DiscoveryDF = NULL

for (i in 971957:972399){
  GSMName <- paste("GSM", i, sep = "") 
  GSM <- getGEO(GSMName, destdir=".")
  DiscoveryDF = rbind(DiscoveryDF, data.frame(Meta(GSM)$characteristics_ch1[1], Meta(GSM)$characteristics_ch1[2],
                                                    Meta(GSM)$characteristics_ch1[3], Meta(GSM)$characteristics_ch1[4],
                                                    Meta(GSM)$characteristics_ch1[8], Meta(GSM)$characteristics_ch1[9],
                                                    Meta(GSM)$characteristics_ch1[11], Meta(GSM)$characteristics_ch1[14],
                                                    Meta(GSM)$characteristics_ch1[15], Meta(GSM)$characteristics_ch1[16],
                                                    Meta(GSM)$characteristics_ch1[18], Meta(GSM)$characteristics_ch1[22],
                                                                                  Meta(GSM)$characteristics_ch1[26]))
}

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## Using locally cached version of GSM972230 found here:
## ./GSM972230.soft

## Using locally cached version of GSM972231 found here:
## ./GSM972231.soft

## Using locally cached version of GSM972232 found here:
## ./GSM972232.soft

## Using locally cached version of GSM972233 found here:
## ./GSM972233.soft

## Using locally cached version of GSM972234 found here:
## ./GSM972234.soft

## Using locally cached version of GSM972235 found here:
## ./GSM972235.soft

## Using locally cached version of GSM972236 found here:
## ./GSM972236.soft

## Using locally cached version of GSM972237 found here:
## ./GSM972237.soft

## Using locally cached version of GSM972238 found here:
## ./GSM972238.soft

## Using locally cached version of GSM972239 found here:
## ./GSM972239.soft

## Using locally cached version of GSM972240 found here:
## ./GSM972240.soft

## Using locally cached version of GSM972241 found here:
## ./GSM972241.soft

## Using locally cached version of GSM972242 found here:
## ./GSM972242.soft

## Using locally cached version of GSM972243 found here:
## ./GSM972243.soft

## Using locally cached version of GSM972244 found here:
## ./GSM972244.soft

## Using locally cached version of GSM972245 found here:
## ./GSM972245.soft

## Using locally cached version of GSM972246 found here:
## ./GSM972246.soft

## Using locally cached version of GSM972247 found here:
## ./GSM972247.soft

## Using locally cached version of GSM972248 found here:
## ./GSM972248.soft

## Using locally cached version of GSM972249 found here:
## ./GSM972249.soft

## Using locally cached version of GSM972250 found here:
## ./GSM972250.soft

## Using locally cached version of GSM972251 found here:
## ./GSM972251.soft

## Using locally cached version of GSM972252 found here:
## ./GSM972252.soft

## Using locally cached version of GSM972253 found here:
## ./GSM972253.soft

## Using locally cached version of GSM972254 found here:
## ./GSM972254.soft

## Using locally cached version of GSM972255 found here:
## ./GSM972255.soft

## Using locally cached version of GSM972256 found here:
## ./GSM972256.soft

## Using locally cached version of GSM972257 found here:
## ./GSM972257.soft

## Using locally cached version of GSM972258 found here:
## ./GSM972258.soft

## Using locally cached version of GSM972259 found here:
## ./GSM972259.soft

## Using locally cached version of GSM972260 found here:
## ./GSM972260.soft

## Using locally cached version of GSM972261 found here:
## ./GSM972261.soft

## Using locally cached version of GSM972262 found here:
## ./GSM972262.soft

## Using locally cached version of GSM972263 found here:
## ./GSM972263.soft

## Using locally cached version of GSM972264 found here:
## ./GSM972264.soft

## Using locally cached version of GSM972265 found here:
## ./GSM972265.soft

## Using locally cached version of GSM972266 found here:
## ./GSM972266.soft

## Using locally cached version of GSM972267 found here:
## ./GSM972267.soft

## Using locally cached version of GSM972268 found here:
## ./GSM972268.soft

## Using locally cached version of GSM972269 found here:
## ./GSM972269.soft

## Using locally cached version of GSM972270 found here:
## ./GSM972270.soft

## Using locally cached version of GSM972271 found here:
## ./GSM972271.soft

## Using locally cached version of GSM972272 found here:
## ./GSM972272.soft

## Using locally cached version of GSM972273 found here:
## ./GSM972273.soft

## Using locally cached version of GSM972274 found here:
## ./GSM972274.soft

## Using locally cached version of GSM972275 found here:
## ./GSM972275.soft

## Using locally cached version of GSM972276 found here:
## ./GSM972276.soft

## Using locally cached version of GSM972277 found here:
## ./GSM972277.soft

## Using locally cached version of GSM972278 found here:
## ./GSM972278.soft

## Using locally cached version of GSM972279 found here:
## ./GSM972279.soft

## Using locally cached version of GSM972280 found here:
## ./GSM972280.soft

## Using locally cached version of GSM972281 found here:
## ./GSM972281.soft

## Using locally cached version of GSM972282 found here:
## ./GSM972282.soft

## Using locally cached version of GSM972283 found here:
## ./GSM972283.soft

## Using locally cached version of GSM972284 found here:
## ./GSM972284.soft

## Using locally cached version of GSM972285 found here:
## ./GSM972285.soft

## Using locally cached version of GSM972286 found here:
## ./GSM972286.soft

## Using locally cached version of GSM972287 found here:
## ./GSM972287.soft

## Using locally cached version of GSM972288 found here:
## ./GSM972288.soft

## Using locally cached version of GSM972289 found here:
## ./GSM972289.soft

## Using locally cached version of GSM972290 found here:
## ./GSM972290.soft

## Using locally cached version of GSM972291 found here:
## ./GSM972291.soft

## Using locally cached version of GSM972292 found here:
## ./GSM972292.soft

## Using locally cached version of GSM972293 found here:
## ./GSM972293.soft

## Using locally cached version of GSM972294 found here:
## ./GSM972294.soft

## Using locally cached version of GSM972295 found here:
## ./GSM972295.soft

## Using locally cached version of GSM972296 found here:
## ./GSM972296.soft

## Using locally cached version of GSM972297 found here:
## ./GSM972297.soft

## Using locally cached version of GSM972298 found here:
## ./GSM972298.soft

## Using locally cached version of GSM972299 found here:
## ./GSM972299.soft

## Using locally cached version of GSM972300 found here:
## ./GSM972300.soft

## Using locally cached version of GSM972301 found here:
## ./GSM972301.soft

## Using locally cached version of GSM972302 found here:
## ./GSM972302.soft

## Using locally cached version of GSM972303 found here:
## ./GSM972303.soft

## Using locally cached version of GSM972304 found here:
## ./GSM972304.soft

## Using locally cached version of GSM972305 found here:
## ./GSM972305.soft

## Using locally cached version of GSM972306 found here:
## ./GSM972306.soft

## Using locally cached version of GSM972307 found here:
## ./GSM972307.soft

## Using locally cached version of GSM972308 found here:
## ./GSM972308.soft

## Using locally cached version of GSM972309 found here:
## ./GSM972309.soft

## Using locally cached version of GSM972310 found here:
## ./GSM972310.soft

## Using locally cached version of GSM972311 found here:
## ./GSM972311.soft

## Using locally cached version of GSM972312 found here:
## ./GSM972312.soft

## Using locally cached version of GSM972313 found here:
## ./GSM972313.soft

## Using locally cached version of GSM972314 found here:
## ./GSM972314.soft

## Using locally cached version of GSM972315 found here:
## ./GSM972315.soft

## Using locally cached version of GSM972316 found here:
## ./GSM972316.soft

## Using locally cached version of GSM972317 found here:
## ./GSM972317.soft

## Using locally cached version of GSM972318 found here:
## ./GSM972318.soft

## Using locally cached version of GSM972319 found here:
## ./GSM972319.soft

## Using locally cached version of GSM972320 found here:
## ./GSM972320.soft

## Using locally cached version of GSM972321 found here:
## ./GSM972321.soft

## Using locally cached version of GSM972322 found here:
## ./GSM972322.soft

## Using locally cached version of GSM972323 found here:
## ./GSM972323.soft

## Using locally cached version of GSM972324 found here:
## ./GSM972324.soft

## Using locally cached version of GSM972325 found here:
## ./GSM972325.soft

## Using locally cached version of GSM972326 found here:
## ./GSM972326.soft

## Using locally cached version of GSM972327 found here:
## ./GSM972327.soft

## Using locally cached version of GSM972328 found here:
## ./GSM972328.soft

## Using locally cached version of GSM972329 found here:
## ./GSM972329.soft

## Using locally cached version of GSM972330 found here:
## ./GSM972330.soft

## Using locally cached version of GSM972331 found here:
## ./GSM972331.soft

## Using locally cached version of GSM972332 found here:
## ./GSM972332.soft

## Using locally cached version of GSM972333 found here:
## ./GSM972333.soft

## Using locally cached version of GSM972334 found here:
## ./GSM972334.soft

## Using locally cached version of GSM972335 found here:
## ./GSM972335.soft

## Using locally cached version of GSM972336 found here:
## ./GSM972336.soft

## Using locally cached version of GSM972337 found here:
## ./GSM972337.soft

## Using locally cached version of GSM972338 found here:
## ./GSM972338.soft

## Using locally cached version of GSM972339 found here:
## ./GSM972339.soft

## Using locally cached version of GSM972340 found here:
## ./GSM972340.soft

## Using locally cached version of GSM972341 found here:
## ./GSM972341.soft

## Using locally cached version of GSM972342 found here:
## ./GSM972342.soft

## Using locally cached version of GSM972343 found here:
## ./GSM972343.soft

## Using locally cached version of GSM972344 found here:
## ./GSM972344.soft

## Using locally cached version of GSM972345 found here:
## ./GSM972345.soft

## Using locally cached version of GSM972346 found here:
## ./GSM972346.soft

## Using locally cached version of GSM972347 found here:
## ./GSM972347.soft

## Using locally cached version of GSM972348 found here:
## ./GSM972348.soft

## Using locally cached version of GSM972349 found here:
## ./GSM972349.soft

## Using locally cached version of GSM972350 found here:
## ./GSM972350.soft

## Using locally cached version of GSM972351 found here:
## ./GSM972351.soft

## Using locally cached version of GSM972352 found here:
## ./GSM972352.soft

## Using locally cached version of GSM972353 found here:
## ./GSM972353.soft

## Using locally cached version of GSM972354 found here:
## ./GSM972354.soft

## Using locally cached version of GSM972355 found here:
## ./GSM972355.soft

## Using locally cached version of GSM972356 found here:
## ./GSM972356.soft

## Using locally cached version of GSM972357 found here:
## ./GSM972357.soft

## Using locally cached version of GSM972358 found here:
## ./GSM972358.soft

## Using locally cached version of GSM972359 found here:
## ./GSM972359.soft

## Using locally cached version of GSM972360 found here:
## ./GSM972360.soft

## Using locally cached version of GSM972361 found here:
## ./GSM972361.soft

## Using locally cached version of GSM972362 found here:
## ./GSM972362.soft

## Using locally cached version of GSM972363 found here:
## ./GSM972363.soft

## Using locally cached version of GSM972364 found here:
## ./GSM972364.soft

## Using locally cached version of GSM972365 found here:
## ./GSM972365.soft

## Using locally cached version of GSM972366 found here:
## ./GSM972366.soft

## Using locally cached version of GSM972367 found here:
## ./GSM972367.soft

## Using locally cached version of GSM972368 found here:
## ./GSM972368.soft

## Using locally cached version of GSM972369 found here:
## ./GSM972369.soft

## Using locally cached version of GSM972370 found here:
## ./GSM972370.soft

## Using locally cached version of GSM972371 found here:
## ./GSM972371.soft

## Using locally cached version of GSM972372 found here:
## ./GSM972372.soft

## Using locally cached version of GSM972373 found here:
## ./GSM972373.soft

## Using locally cached version of GSM972374 found here:
## ./GSM972374.soft

## Using locally cached version of GSM972375 found here:
## ./GSM972375.soft

## Using locally cached version of GSM972376 found here:
## ./GSM972376.soft

## Using locally cached version of GSM972377 found here:
## ./GSM972377.soft

## Using locally cached version of GSM972378 found here:
## ./GSM972378.soft

## Using locally cached version of GSM972379 found here:
## ./GSM972379.soft

## Using locally cached version of GSM972380 found here:
## ./GSM972380.soft

## Using locally cached version of GSM972381 found here:
## ./GSM972381.soft

## Using locally cached version of GSM972382 found here:
## ./GSM972382.soft

## Using locally cached version of GSM972383 found here:
## ./GSM972383.soft

## Using locally cached version of GSM972384 found here:
## ./GSM972384.soft

## Using locally cached version of GSM972385 found here:
## ./GSM972385.soft

## Using locally cached version of GSM972386 found here:
## ./GSM972386.soft

## Using locally cached version of GSM972387 found here:
## ./GSM972387.soft

## Using locally cached version of GSM972388 found here:
## ./GSM972388.soft

## Using locally cached version of GSM972389 found here:
## ./GSM972389.soft

## Using locally cached version of GSM972390 found here:
## ./GSM972390.soft

## Using locally cached version of GSM972391 found here:
## ./GSM972391.soft

## Using locally cached version of GSM972392 found here:
## ./GSM972392.soft

## Using locally cached version of GSM972393 found here:
## ./GSM972393.soft

## Using locally cached version of GSM972394 found here:
## ./GSM972394.soft

## Using locally cached version of GSM972395 found here:
## ./GSM972395.soft

## Using locally cached version of GSM972396 found here:
## ./GSM972396.soft

## Using locally cached version of GSM972397 found here:
## ./GSM972397.soft

## Using locally cached version of GSM972398 found here:
## ./GSM972398.soft

## Using locally cached version of GSM972399 found here:
## ./GSM972399.soft

##Now, cleanup the age column b/c it's entered as a string and we'll need numbers

#Remove "dataset: validation"
AgeVecTrun <- gsub("^.*?age.at.diagnosis: ","",DiscoveryDF$Meta.GSM..characteristics_ch1.3.)

#Remove quotes
AgeVecnoquote <- noquote(AgeVecTrun)

#Consider as numeric
AgeVecNumeric <- as.numeric(unlist(AgeVecnoquote))

#Ignore NAs
AgeVecNumeric <- AgeVecNumeric[!is.na(AgeVecNumeric)]


###Now, cleanup OS.delay column
OSVecTrun <- gsub("^.*?os.delay: ","",DiscoveryDF$Meta.GSM..characteristics_ch1.14.)

#Remove quotes
OSVecnoquote <- noquote(OSVecTrun)

#Consider as numeric
OSVecNumeric <- as.numeric(unlist(OSVecnoquote))

#Ignore NAs
OSVecNumeric <- OSVecNumeric[!is.na(OSVecNumeric)]

###Find avg, stdev, and range for age in years
round(mean(AgeVecNumeric),0)

## [1] 67

round(sd(AgeVecNumeric),0)

## [1] 14

round(range(AgeVecNumeric),0)

## [1] 22 97

###Find # of M/F and %

#Male #
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.2. == "Sex: M", na.rm=TRUE),0)

## [1] 237

#Female #
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.2. == "Sex: F", na.rm=TRUE),0)

## [1] 206

#Male %
round(((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.2. == "Sex: M", na.rm=TRUE)/443)*100),0)

## [1] 53

#Female %
round(((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.2. == "Sex: F", na.rm=TRUE)/443)*100),0)

## [1] 47

###Find # and % of stage I, II, II, IV individuals

#Stage 1 #, note that the authors include the four stage 0 values, so there are
#actually only 24 instances of stage I
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 0", na.rm=TRUE) +
  sum(DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 1", na.rm=TRUE),0)

## [1] 27

#Stage 1 %
round((((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 0", na.rm=TRUE) +
  sum(DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 1", na.rm=TRUE))/ 443)*100),0)

## [1] 6

#Stage 2 #
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE),0)

## [1] 198

#Stage 2 %
round(((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE)/443)*100),0)

## [1] 45

#Stage 3 #
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE),0)

## [1] 164

#Stage 3 %
round(((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE)/443)*100),0)

## [1] 37

#Stage 4 #
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 4", na.rm=TRUE),0)

## [1] 54

#Stage 4 %
round(((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 4", na.rm=TRUE)/443)*100),0)

## [1] 12

###Find # located at proximal or distal & %

#Proximal #
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.8. == "tumor.location: proximal", na.rm=TRUE),0)

## [1] 176

#Proximal %
round(((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.8. == "tumor.location: proximal", na.rm=TRUE)/443)*100),0)

## [1] 40

#Distal #
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.8. == "tumor.location: distal", na.rm=TRUE),0)

## [1] 267

#Distal %
round(((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.8. == "tumor.location: distal", na.rm=TRUE)/443)*100),0)

## [1] 60

###Find # and % w/ adjuvant chemo

#Adjuvant chemo # Y
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.9. == "chemotherapy.adjuvant: Y" &
            DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE) +
sum(DiscoveryDF$Meta.GSM..characteristics_ch1.9. == "chemotherapy.adjuvant: Y" &
            DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE),0)

## [1] 161

#Adjuvant chemo % Y
ceiling((round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.9. == "chemotherapy.adjuvant: Y" &
                   DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE) +
               sum(DiscoveryDF$Meta.GSM..characteristics_ch1.9. == "chemotherapy.adjuvant: Y" &
                     DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE),0)/362)*100)

## [1] 45

#Adjuvant chemo # N
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.9. == "chemotherapy.adjuvant: N" &
            DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE) +
        sum(DiscoveryDF$Meta.GSM..characteristics_ch1.9. == "chemotherapy.adjuvant: N" &
              DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE),0)

## [1] 200

#Adjuvant chemo % N
round((round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.9. == "chemotherapy.adjuvant: N" &
                   DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE) +
               sum(DiscoveryDF$Meta.GSM..characteristics_ch1.9. == "chemotherapy.adjuvant: N" &
                     DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE),0)/362)*100,0)

## [1] 55

###Find median follow-up with stdev and range in months
median(OSVecNumeric)

## [1] 50

round(sd(OSVecNumeric),0)

## [1] 39

range(OSVecNumeric)

## [1]   0 201

###Find relapse # & %
###Note: the authors provide data for distant/locorgional/both in the paper,
###but I don't see this info in the metadata for me to evaluate
#No. Y
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.11. == "rfs.event: 1" &
            DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE) +
        sum(DiscoveryDF$Meta.GSM..characteristics_ch1.11. == "rfs.event: 1" &
              DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE),0)

## [1] 109

#% Y
round((round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.11. == "rfs.event: 1" &
                   DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE) +
               sum(DiscoveryDF$Meta.GSM..characteristics_ch1.11. == "rfs.event: 1" &
                     DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE),0)/362)*100,0)

## [1] 30

#No. N
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.11. == "rfs.event: 0" &
            DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE) +
        sum(DiscoveryDF$Meta.GSM..characteristics_ch1.11. == "rfs.event: 0" &
              DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE),0)

## [1] 250

#% N
ceiling((round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.11. == "rfs.event: 0" &
                     DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE) +
                 sum(DiscoveryDF$Meta.GSM..characteristics_ch1.11. == "rfs.event: 0" &
                       DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE),0)/362)*100)

## [1] 70

#No. NA
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.11. == "rfs.event: NA" &
            DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 2", na.rm=TRUE) +
        sum(DiscoveryDF$Meta.GSM..characteristics_ch1.11. == "rfs.event: NA" &
              DiscoveryDF$Meta.GSM..characteristics_ch1.4. == "tnm.stage: 3", na.rm=TRUE),0)

## [1] 3

###Find # and % dMMR

#No. dMMR
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.15. == "mmr.status: dMMR", na.rm=TRUE),0)

## [1] 61

#% dMMR
#First, subtract NAs from total sample size
443-round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.15. == "mmr.status: NA", na.rm=TRUE),0)

## [1] 409

#Now find %
round((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.15. == "mmr.status: dMMR", na.rm=TRUE))/
    (443-sum(DiscoveryDF$Meta.GSM..characteristics_ch1.15. == "mmr.status: NA", na.rm=TRUE))*100,0)

## [1] 15

###Find # and % CIMP+
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.16. == "cimp.status: +", na.rm=TRUE),0)

## [1] 74

#% CIMP+
#First, subtract NAs from total sample size
443-round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.16. == "cimp.status: NA", na.rm=TRUE),0)

## [1] 380

#Now find %
round((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.16. == "cimp.status: +", na.rm=TRUE))/
        (443-sum(DiscoveryDF$Meta.GSM..characteristics_ch1.16. == "cimp.status: NA", na.rm=TRUE))*100,0)

## [1] 19

###Find # and % KRAS-mutant
#No. KRAS-mutant
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.22. == "kras.mutation: M", na.rm=TRUE),0)

## [1] 172

#% KRAS-mutant
#First, subtract NAs from total sample size
#Note: the authors mistakenly switched the total sample size for the kras and BRAF mutations
443-round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.22. == "kras.mutation: NA", na.rm=TRUE),0)

## [1] 424

#Now find %
round((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.22. == "kras.mutation: M", na.rm=TRUE))/
        (443-sum(DiscoveryDF$Meta.GSM..characteristics_ch1.22. == "kras.mutation: NA", na.rm=TRUE))*100,0)

## [1] 41

###Find # and % BRAF-mutant
#No. BRAF-mutant
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.26. == "braf.mutation: M", na.rm=TRUE),0)

## [1] 44

#% BRAF-mutant
#First, subtract NAs from total sample size
443-round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.26. == "braf.mutation: NA", na.rm=TRUE),0)

## [1] 392

#Now find %
round((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.26. == "braf.mutation: M", na.rm=TRUE))/
        (443-sum(DiscoveryDF$Meta.GSM..characteristics_ch1.26. == "braf.mutation: NA", na.rm=TRUE))*100,0)

## [1] 11

###Find # and % TP53-mutant
#No. TP53-mutant
round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.18. == "tp53.mutation: M", na.rm=TRUE),0)

## [1] 135

#% TP53-mutant
#First, subtract NAs from total sample size
443-round(sum(DiscoveryDF$Meta.GSM..characteristics_ch1.18. == "tp53.mutation: NA", na.rm=TRUE),0)

## [1] 245

#Now find %
round((sum(DiscoveryDF$Meta.GSM..characteristics_ch1.18. == "tp53.mutation: M", na.rm=TRUE))/
        (443-sum(DiscoveryDF$Meta.GSM..characteristics_ch1.18. == "tp53.mutation: NA", na.rm=TRUE))*100,0)

## [1] 55

Maris_2013_Table_1_Discovery

Abby Moore

June 12, 2017