Load the vcfR package with library()`:
library(vegan)## Warning: package 'vegan' was built under R version 4.2.2## Loading required package: permute## Loading required package: lattice## This is vegan 2.6-4library(ggplot2)
library(ggpubr)##Confirm File Locations and Working Directory
getwd()## [1] "C:/Users/Owner/Downloads"list.files(pattern = "vcf")## [1] "1.159051856-159301856.ALL.chr1_GRCh38.genotypes.20170504.vcf.gz"
## [2] "17.29734902-2997490.vcf"
## [3] "17.29734902-29974902.ALL.chr17_GRCh38.genotypes.20170504.vcf.gz"
## [4] "ALL.chr17_GRCh38.genotypes.20170504.vcf.gz"
## [5] "all_loci.vcf"
## [6] "code_checkpoint_vcfR--1-.html"
## [7] "code_checkpoint_vcfR (1).Rmd"
## [8] "code_checkpoint_vcfR.html"
## [9] "code_checkpoint_vcfR.Rmd"
## [10] "my_snps.vcf.gz"
## [11] "PCA-on-SNPs-data-from-a-vcf-file-Part-1---Data-Preparation.html"
## [12] "PCA on SNPs data from a vcf file Part 1 - Data Preparation.Rmd"
## [13] "vcf_num.csv"
## [14] "vcf_num_df.csv"
## [15] "vcf_num_df2.csv"
## [16] "vcfR_test.vcf"
## [17] "vcfR_test.vcf.gz"##SNP Data Setup ###Load your personal SNP file
vcf <- vcfR::read.vcfR("my_snps.vcf.gz", convertNA = TRUE)## Scanning file to determine attributes.
## File attributes:
## meta lines: 130
## header_line: 131
## variant count: 5340
## column count: 2513
##
Meta line 130 read in.
## All meta lines processed.
## gt matrix initialized.
## Character matrix gt created.
## Character matrix gt rows: 5340
## Character matrix gt cols: 2513
## skip: 0
## nrows: 5340
## row_num: 0
##
Processed variant 1000
Processed variant 2000
Processed variant 3000
Processed variant 4000
Processed variant 5000
Processed variant: 5340
## All variants processedWe should have 5340 variants processed. Does this match?
##Convert Raw VCF file –> Genotype Scores ###Get genotype scores (allele counts)
vcf_num <- vcfR::extract.gt(vcf,
element = "GT",
IDtoRowNames = F,
as.numeric = T,
convertNA = T)###Save the CSV
write.csv(vcf_num, file = "vcf_num.csv", row.names = F)###Confirm that it is in your Files
list.files(pattern = "vcf")## [1] "1.159051856-159301856.ALL.chr1_GRCh38.genotypes.20170504.vcf.gz"
## [2] "17.29734902-2997490.vcf"
## [3] "17.29734902-29974902.ALL.chr17_GRCh38.genotypes.20170504.vcf.gz"
## [4] "ALL.chr17_GRCh38.genotypes.20170504.vcf.gz"
## [5] "all_loci.vcf"
## [6] "code_checkpoint_vcfR--1-.html"
## [7] "code_checkpoint_vcfR (1).Rmd"
## [8] "code_checkpoint_vcfR.html"
## [9] "code_checkpoint_vcfR.Rmd"
## [10] "my_snps.vcf.gz"
## [11] "PCA-on-SNPs-data-from-a-vcf-file-Part-1---Data-Preparation.html"
## [12] "PCA on SNPs data from a vcf file Part 1 - Data Preparation.Rmd"
## [13] "vcf_num.csv"
## [14] "vcf_num_df.csv"
## [15] "vcf_num_df2.csv"
## [16] "vcfR_test.vcf"
## [17] "vcfR_test.vcf.gz"##Transpose Original VCF Orientation to R Dataframe
vcf_num_t <- t(vcf_num)###Make it into a dataframe
vcf_num_df <- data.frame(vcf_num_t)###Add row names into data frame as column that can be removed
sample <- row.names(vcf_num_df)vcf_num_df <- data.frame(sample, vcf_num_df)write.csv(vcf_num_df, file = "vcf_num_df.csv", row.names = F)
list.files(pattern = "csv")## [1] "1000genomes_people_info2-1.csv" "cleaned_data.csv"
## [3] "dinog.csv" "gwas_pheno_env.csv"
## [5] "pheno.csv" "SNPs_cleaned.csv"
## [7] "vcf_num.csv" "vcf_num_df.csv"
## [9] "vcf_num_df2.csv" "walsh2017morphology.csv"##Clean the Data
Load the population meta data
pop_meta <- read.csv("1000genomes_people_info2-1.csv")###Check to make sure that “sample” column is in meta/SNP data
names(pop_meta)## [1] "pop" "super_pop" "sample" "sex" "lat" "lng"names(vcf_num_df)[1:10]## [1] "sample" "X1" "X2" "X3" "X4" "X5" "X6" "X7"
## [9] "X8" "X9"###Merge the two data sets together
vcf_num_df2 <- merge(pop_meta,
vcf_num_df,
by = "sample")###Check the dimensions before/after merge
nrow(vcf_num_df) == nrow(vcf_num_df2)## [1] TRUE###Check new dataframe names
names(vcf_num_df2)[1:15]## [1] "sample" "pop" "super_pop" "sex" "lat" "lng"
## [7] "X1" "X2" "X3" "X4" "X5" "X6"
## [13] "X7" "X8" "X9"write.csv(vcf_num_df2, file = "vcf_num_df2.csv", row.names = F)
list.files(pattern = "csv")## [1] "1000genomes_people_info2-1.csv" "cleaned_data.csv"
## [3] "dinog.csv" "gwas_pheno_env.csv"
## [5] "pheno.csv" "SNPs_cleaned.csv"
## [7] "vcf_num.csv" "vcf_num_df.csv"
## [9] "vcf_num_df2.csv" "walsh2017morphology.csv"##Omit Invariant Features ###Omit any invariant data so there is no scaling issues later
invar_omit <- function(x){
cat("Dataframe of dim", dim(x), "procedded...\n")
sds <- apply(x, 2, sd, na.rm = TRUE)
i_var0 <- which(sds == 0)
cat(length(i_var0), "columns removed\n")
if(length(i_var0) > 0){
x <- x[,-i_var0]
}
return(x)
}names(vcf_num_df2)[1:10]## [1] "sample" "pop" "super_pop" "sex" "lat" "lng"
## [7] "X1" "X2" "X3" "X4"Run this function ONLY on numeric column data
vcf_noinvar <- vcf_num_df2vcf_noinvar[, -c(1:6)] <- invar_omit(vcf_noinvar[, -c(1:6)])## Dataframe of dim 2504 5340 procedded...
## 1493 columns removed###How many columns were removed? ###Create an object that holds the number of invariant columns removed
my_meta_N_invar_cols <- 1493##Remove Low Quality Data ###Poor Quality can result in a skew of the data We must remove the rows of NAs!
find_NAs <- function(x){
NAs_TF <- is.na(x)
i_NA <- which(NAs_TF == TRUE)
N_NA <- length(i_NA)
return(i_NA)
}###Search for the NAs with the for() loop
# N_rows
# number of rows (individuals)
N_rows <- nrow(vcf_noinvar)
# N_NA
# vector to hold output (number of NAs)
N_NA <- rep(x = 0, times = N_rows)
# N_SNPs
# total number of columns (SNPs)
N_SNPs <- ncol(vcf_noinvar)
# the for() loop
for(i in 1:N_rows){
# for each row, find the location of
## NAs with vcf_noinvar()
i_NA <- find_NAs(vcf_noinvar[i,])
# then determine how many NAs
## with length()
N_NA_i <- length(i_NA)
# then save the output to
## our storage vector
N_NA[i] <- N_NA_i
}###Check for rows with >50% NAs
cutoff50 <- N_SNPs*0.5
percent_NA <- N_NA/N_SNPs*100
any(percent_NA > 50)## [1] FALSECheck average number of NAs per row
mean(percent_NA)## [1] 0Save the mean percent of NAs per row
my_meta_N_meanNA_rows <- mean(percent_NA)##Imputation of NAs ###Perform our mean imputation to ensure we have a mean of 0
mean_imputation <- function(df){
n_cols <- ncol(df)
for(i in 1:n_cols){
column_i <- df[, i]
mean_i <- mean(column_i, na.rm = TRUE)
NAs_i <- which(is.na(column_i))
N_NAs <- length(NAs_i)
column_i[NAs_i] <- mean_i
df[, i] <- column_i
}
return(df)
}names(vcf_noinvar)[1:10]## [1] "sample" "pop" "super_pop" "sex" "lat" "lng"
## [7] "X1" "X2" "X3" "X4"###Only run on numeric columns
vcf_noNA <- vcf_noinvar
vcf_noNA[, -c(1:6)] <- mean_imputation(vcf_noinvar[,-c(1:6)])##PCA Preparation ###Scale data for PCA
vcf_scaled <- vcf_noNAhead(vcf_scaled)## sample pop super_pop sex lat lng X1 X2 X3 X4 X5 X6 X7 X8 X9
## 1 HG00096 GBR EUR male 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## 2 HG00097 GBR EUR female 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## 3 HG00099 GBR EUR female 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## 4 HG00100 GBR EUR female 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## 5 HG00101 GBR EUR male 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## 6 HG00102 GBR EUR female 52.48624 -1.890401 0 0 0 0 0 0 0 0 0
## X10 X11 X12 X13 X14 X15 X16 X17 X18 X19 X20 X21 X22 X23 X24 X25 X26 X27 X28
## 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1
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## X1302 X1303 X1304 X1305 X1306 X1307 X1308 X1309 X1310 X1311 X1312 X1313 X1314
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1315 X1316 X1317 X1318 X1319 X1320 X1321 X1322 X1323 X1324 X1325 X1326 X1327
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1328 X1329 X1330 X1331 X1332 X1333 X1334 X1335 X1336 X1337 X1338 X1339 X1340
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1341 X1342 X1343 X1344 X1345 X1346 X1347 X1348 X1349 X1350 X1351 X1352 X1353
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 1 0 0 0 0 0 0 0 0 0
## 3 0 0 0 1 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 1 0 0 0 0 0 0 0 0 0
## X1354 X1355 X1356 X1357 X1358 X1359 X1360 X1361 X1362 X1363 X1364 X1365 X1366
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 1 0 0 0
## 3 0 0 0 0 0 0 0 0 0 1 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 1 0 0 0
## X1367 X1368 X1369 X1370 X1371 X1372 X1373 X1374 X1375 X1376 X1377 X1378 X1379
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1380 X1381 X1382 X1383 X1384 X1385 X1386 X1387 X1388 X1389 X1390 X1391 X1392
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 1 0 0 0 0 0 0
## 3 0 0 0 0 0 0 1 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 1 0 0 0 0 0 0
## X1393 X1394 X1395 X1396 X1397 X1398 X1399 X1400 X1401 X1402 X1403 X1404 X1405
## 1 0 0 0 0 0 1 0 0 0 0 0 0 0
## 2 0 0 0 0 0 1 0 0 0 0 0 0 0
## 3 0 0 0 0 0 1 0 0 0 0 0 0 0
## 4 0 0 0 0 0 1 0 0 0 0 0 0 0
## 5 0 0 0 0 0 1 0 0 0 0 0 0 0
## 6 0 0 0 0 0 1 0 0 0 0 0 0 0
## X1406 X1407 X1408 X1409 X1410 X1411 X1412 X1413 X1414 X1415 X1416 X1417 X1418
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 1 0 0 0 0 0 0 0 0
## 3 0 0 0 0 1 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 1 0 0 0 0 0 0 0 0
## X1419 X1420 X1421 X1422 X1423 X1424 X1425 X1426 X1427 X1428 X1429 X1430 X1431
## 1 0 0 0 0 0 1 0 0 0 0 1 0 0
## 2 0 0 0 0 0 0 0 0 0 0 1 0 0
## 3 0 0 0 0 0 0 0 0 0 0 1 0 0
## 4 0 0 0 0 0 1 0 0 0 0 0 0 0
## 5 0 0 0 0 0 1 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 1 0 0
## X1432 X1433 X1434 X1435 X1436 X1437 X1438 X1439 X1440 X1441 X1442 X1443 X1444
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 1 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1445 X1446 X1447 X1448 X1449 X1450 X1451 X1452 X1453 X1454 X1455 X1456 X1457
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1458 X1459 X1460 X1461 X1462 X1463 X1464 X1465 X1466 X1467 X1468 X1469 X1470
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1471 X1472 X1473 X1474 X1475 X1476 X1477 X1478 X1479 X1480 X1481 X1482 X1483
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1484 X1485 X1486 X1487 X1488 X1489 X1490 X1491 X1492 X1493 X1494 X1495 X1496
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1497 X1498 X1499 X1500 X1501 X1502 X1503 X1504 X1505 X1506 X1507 X1508 X1509
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1510 X1511 X1512 X1513 X1514 X1515 X1516 X1517 X1518 X1519 X1520 X1521 X1522
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1523 X1524 X1525 X1526 X1527 X1528 X1529 X1530 X1531 X1532 X1533 X1534 X1535
## 1 0 0 0 1 1 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 1 0 0 0 0 0 0 0 0
## 5 0 0 0 0 1 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1536 X1537 X1538 X1539 X1540 X1541 X1542 X1543 X1544 X1545 X1546 X1547 X1548
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1549 X1550 X1551 X1552 X1553 X1554 X1555 X1556 X1557 X1558 X1559 X1560 X1561
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 1 0 0 1 0 0 0 0 0
## 3 0 0 0 0 1 0 0 1 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 1 0 0 1 0 0 0 0 0
## X1562 X1563 X1564 X1565 X1566 X1567 X1568 X1569 X1570 X1571 X1572 X1573 X1574
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1575 X1576 X1577 X1578 X1579 X1580 X1581 X1582 X1583 X1584 X1585 X1586 X1587
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1588 X1589 X1590 X1591 X1592 X1593 X1594 X1595 X1596 X1597 X1598 X1599 X1600
## 1 0 0 1 0 0 0 0 0 0 0 0 0 0
## 2 0 0 1 0 0 0 0 0 0 0 0 0 1
## 3 0 0 1 0 0 0 0 0 0 0 0 0 1
## 4 0 0 1 0 0 0 0 0 0 0 0 0 0
## 5 0 0 1 0 0 0 0 0 0 0 0 0 0
## 6 0 0 1 0 0 0 0 0 0 0 0 0 1
## X1601 X1602 X1603 X1604 X1605 X1606 X1607 X1608 X1609 X1610 X1611 X1612 X1613
## 1 0 1 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1614 X1615 X1616 X1617 X1618 X1619 X1620 X1621 X1622 X1623 X1624 X1625 X1626
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 1 0 0 0 0 0 0 0 0
## 3 0 0 0 0 1 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 1 0 0 0 0 0 0 0 0
## X1627 X1628 X1629 X1630 X1631 X1632 X1633 X1634 X1635 X1636 X1637 X1638 X1639
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 1
## 3 0 0 0 0 0 0 0 0 0 0 0 0 1
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 1
## X1640 X1641 X1642 X1643 X1644 X1645 X1646 X1647 X1648 X1649 X1650 X1651 X1652
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 1 0 0 0 0 0 0 0 0
## 3 0 0 0 0 1 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 1 0 0 0 0 0 0 0 0
## X1653 X1654 X1655 X1656 X1657 X1658 X1659 X1660 X1661 X1662 X1663 X1664 X1665
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 1 0 0 0 0 0 0 0 0 0 0 0
## 3 0 1 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 1 0 0 0 0 0 0 0 0 0 0 0
## X1666 X1667 X1668 X1669 X1670 X1671 X1672 X1673 X1674 X1675 X1676 X1677 X1678
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1679 X1680 X1681 X1682 X1683 X1684 X1685 X1686 X1687 X1688 X1689 X1690 X1691
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 1 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1692 X1693 X1694 X1695 X1696 X1697 X1698 X1699 X1700 X1701 X1702 X1703 X1704
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1705 X1706 X1707 X1708 X1709 X1710 X1711 X1712 X1713 X1714 X1715 X1716 X1717
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 1 0 0 0 0 1 0
## 3 0 0 0 0 0 0 1 0 0 0 0 1 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 1 0 0 0 0 1 0
## X1718 X1719 X1720 X1721 X1722 X1723 X1724 X1725 X1726 X1727 X1728 X1729 X1730
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 1 0 0 0 1 0 0 1 1 1
## 3 0 0 0 1 0 0 0 1 0 0 1 1 1
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 1 0 0 0 1 0 0 1 1 1
## X1731 X1732 X1733 X1734 X1735 X1736 X1737 X1738 X1739 X1740 X1741 X1742 X1743
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 1 0 0
## 3 0 0 0 0 0 0 0 0 0 0 1 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 1 0 0
## X1744 X1745 X1746 X1747 X1748 X1749 X1750 X1751 X1752 X1753 X1754 X1755 X1756
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 1 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 1 0 0 0
## X1757 X1758 X1759 X1760 X1761 X1762 X1763 X1764 X1765 X1766 X1767 X1768 X1769
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1770 X1771 X1772 X1773 X1774 X1775 X1776 X1777 X1778 X1779 X1780 X1781 X1782
## 1 0 0 0 0 1 0 0 0 0 0 0 0 0
## 2 0 0 0 0 1 0 0 0 0 0 0 0 0
## 3 0 0 0 0 1 0 0 0 0 0 0 0 0
## 4 0 0 0 0 1 0 0 0 0 0 0 0 0
## 5 0 0 0 0 1 0 0 0 0 0 0 0 0
## 6 0 0 0 0 1 0 0 0 0 0 0 0 0
## X1783 X1784 X1785 X1786 X1787 X1788 X1789 X1790 X1791 X1792 X1793 X1794 X1795
## 1 0 0 0 1 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 1 0 0 1 0 0 0 1 0
## 3 0 0 0 0 1 0 0 1 0 0 0 1 0
## 4 0 0 0 1 0 0 0 0 0 0 0 0 0
## 5 0 0 0 1 0 0 0 0 0 0 0 0 0
## 6 0 0 1 0 1 0 0 1 0 0 0 1 0
## X1796 X1797 X1798 X1799 X1800 X1801 X1802 X1803 X1804 X1805 X1806 X1807 X1808
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1809 X1810 X1811 X1812 X1813 X1814 X1815 X1816 X1817 X1818 X1819 X1820 X1821
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 1 0 0 0 0
## 3 0 0 0 0 0 0 0 0 1 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 1 0 0 0 0
## X1822 X1823 X1824 X1825 X1826 X1827 X1828 X1829 X1830 X1831 X1832 X1833 X1834
## 1 0 0 0 0 0 0 0 0 0 0 1 0 0
## 2 0 0 0 0 0 0 1 0 0 0 0 0 0
## 3 0 0 0 0 0 0 1 0 0 0 1 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 1 0 0 0 1 0 0
## X1835 X1836 X1837 X1838 X1839 X1840 X1841 X1842 X1843 X1844 X1845 X1846 X1847
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1848 X1849 X1850 X1851 X1852 X1853 X1854 X1855 X1856 X1857 X1858 X1859 X1860
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 1 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1861 X1862 X1863 X1864 X1865 X1866 X1867 X1868 X1869 X1870 X1871 X1872 X1873
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 1 0 0 0 0 0 0 0 0 1
## 3 0 0 0 1 0 0 0 0 0 0 0 0 1
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 1 0 0 0 0 0 0 0 0 1
## X1874 X1875 X1876 X1877 X1878 X1879 X1880 X1881 X1882 X1883 X1884 X1885 X1886
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1887 X1888 X1889 X1890 X1891 X1892 X1893 X1894 X1895 X1896 X1897 X1898 X1899
## 1 0 0 1 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1900 X1901 X1902 X1903 X1904 X1905 X1906 X1907 X1908 X1909 X1910 X1911 X1912
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1913 X1914 X1915 X1916 X1917 X1918 X1919 X1920 X1921 X1922 X1923 X1924 X1925
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1926 X1927 X1928 X1929 X1930 X1931 X1932 X1933 X1934 X1935 X1936 X1937 X1938
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 1 0 1 0 0
## 3 0 0 0 0 0 0 0 0 1 0 1 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 1 0 1 0 0
## X1939 X1940 X1941 X1942 X1943 X1944 X1945 X1946 X1947 X1948 X1949 X1950 X1951
## 1 0 0 0 0 0 0 0 1 0 0 0 0 0
## 2 0 0 0 1 0 0 0 1 0 0 0 0 0
## 3 0 0 0 1 0 0 0 1 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 1 0 0 0 1 0 0 0 0 0
## X1952 X1953 X1954 X1955 X1956 X1957 X1958 X1959 X1960 X1961 X1962 X1963 X1964
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X1965 X1966 X1967 X1968 X1969 X1970 X1971 X1972 X1973 X1974 X1975 X1976 X1977
## 1 0 0 1 0 0 0 0 0 0 0 0 0 0
## 2 0 0 1 0 0 0 0 0 0 0 0 0 0
## 3 0 0 1 0 0 0 0 0 0 0 0 0 0
## 4 0 0 1 0 0 0 0 0 0 0 0 0 0
## 5 0 0 1 0 0 0 0 0 0 0 0 0 0
## 6 0 0 1 0 0 0 0 0 0 0 0 0 0
## X1978 X1979 X1980 X1981 X1982 X1983 X1984 X1985 X1986 X1987 X1988 X1989 X1990
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 1 0 0 0 0
## 3 0 0 0 0 0 0 0 0 1 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 1 0 0 0 0
## X1991 X1992 X1993 X1994 X1995 X1996 X1997 X1998 X1999 X2000 X2001 X2002 X2003
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 1 0 0 0 0 0 0 0 0
## 3 0 0 0 0 1 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 1 0 0 0 0 0 0 0 0
## X2004 X2005 X2006 X2007 X2008 X2009 X2010 X2011 X2012 X2013 X2014 X2015 X2016
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 1 0 0 1 0
## 3 0 0 0 0 0 0 0 0 1 0 0 1 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 1 0 0 1 0
## X2017 X2018 X2019 X2020 X2021 X2022 X2023 X2024 X2025 X2026 X2027 X2028 X2029
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 1
## 3 0 0 0 0 0 0 0 0 0 0 0 0 1
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 1
## X2030 X2031 X2032 X2033 X2034 X2035 X2036 X2037 X2038 X2039 X2040 X2041 X2042
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 1 0 0 1 0 1 0 0
## 3 0 0 0 0 0 1 0 0 1 0 1 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 1 0 0 1 0 1 0 0
## X2043 X2044 X2045 X2046 X2047 X2048 X2049 X2050 X2051 X2052 X2053 X2054 X2055
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## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X4994 X4995 X4996 X4997 X4998 X4999 X5000 X5001 X5002 X5003 X5004 X5005 X5006
## 1 1 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 1 0 0 0 0 0 0 0 0 0 0 0 0
## 5 1 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5007 X5008 X5009 X5010 X5011 X5012 X5013 X5014 X5015 X5016 X5017 X5018 X5019
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5020 X5021 X5022 X5023 X5024 X5025 X5026 X5027 X5028 X5029 X5030 X5031 X5032
## 1 0 0 0 0 0 0 0 0 0 0 1 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 1 0 0
## 5 0 0 0 0 0 0 0 0 0 0 1 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5033 X5034 X5035 X5036 X5037 X5038 X5039 X5040 X5041 X5042 X5043 X5044 X5045
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5046 X5047 X5048 X5049 X5050 X5051 X5052 X5053 X5054 X5055 X5056 X5057 X5058
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5059 X5060 X5061 X5062 X5063 X5064 X5065 X5066 X5067 X5068 X5069 X5070 X5071
## 1 0 1 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 1 0 0 0 0 0 0 0 0 0 0 0
## 5 0 1 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5072 X5073 X5074 X5075 X5076 X5077 X5078 X5079 X5080 X5081 X5082 X5083 X5084
## 1 0 0 0 0 0 0 0 0 0 0 0 0 1
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 1
## 5 0 0 0 0 0 0 0 0 0 0 0 0 1
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5085 X5086 X5087 X5088 X5089 X5090 X5091 X5092 X5093 X5094 X5095 X5096 X5097
## 1 0 0 0 0 0 0 0 0 0 0 1 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 1 0 0
## 5 0 0 0 0 0 0 0 0 0 0 1 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5098 X5099 X5100 X5101 X5102 X5103 X5104 X5105 X5106 X5107 X5108 X5109 X5110
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5111 X5112 X5113 X5114 X5115 X5116 X5117 X5118 X5119 X5120 X5121 X5122 X5123
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 1
## 3 0 0 0 0 0 0 0 0 0 0 0 0 1
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 1
## X5124 X5125 X5126 X5127 X5128 X5129 X5130 X5131 X5132 X5133 X5134 X5135 X5136
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 1 0 0 0 0 0
## 3 0 0 0 0 0 0 0 1 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 1 0 0 0 0 0
## X5137 X5138 X5139 X5140 X5141 X5142 X5143 X5144 X5145 X5146 X5147 X5148 X5149
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5150 X5151 X5152 X5153 X5154 X5155 X5156 X5157 X5158 X5159 X5160 X5161 X5162
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5163 X5164 X5165 X5166 X5167 X5168 X5169 X5170 X5171 X5172 X5173 X5174 X5175
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5176 X5177 X5178 X5179 X5180 X5181 X5182 X5183 X5184 X5185 X5186 X5187 X5188
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5189 X5190 X5191 X5192 X5193 X5194 X5195 X5196 X5197 X5198 X5199 X5200 X5201
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 1 0 0 0 0 0 0 0 0 0 0
## 3 0 0 1 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 1 0 0 0 0 0 0 0 0 0 0
## X5202 X5203 X5204 X5205 X5206 X5207 X5208 X5209 X5210 X5211 X5212 X5213 X5214
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 1 0 0 0 0
## 3 0 0 0 0 0 0 0 0 1 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 1 0 0 0 0
## X5215 X5216 X5217 X5218 X5219 X5220 X5221 X5222 X5223 X5224 X5225 X5226 X5227
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5228 X5229 X5230 X5231 X5232 X5233 X5234 X5235 X5236 X5237 X5238 X5239 X5240
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 1 0 0 0 0 0 0 0
## 3 0 0 0 0 0 1 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
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## 6 0 0 0 0 0 1 0 0 0 0 0 0 0
## X5241 X5242 X5243 X5244 X5245 X5246 X5247 X5248 X5249 X5250 X5251 X5252 X5253
## 1 0 0 0 0 1 0 0 0 0 0 0 0 0
## 2 0 0 0 0 1 0 0 0 0 0 0 0 0
## 3 0 0 0 0 1 0 0 0 0 0 0 0 0
## 4 0 0 0 0 1 0 0 0 0 0 0 0 0
## 5 0 0 0 0 1 0 0 0 0 0 0 0 0
## 6 0 0 0 0 1 0 0 0 0 0 0 0 0
## X5254 X5255 X5256 X5257 X5258 X5259 X5260 X5261 X5262 X5263 X5264 X5265 X5266
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 1 0 0 0 0 0 0 0 0 0
## 3 0 0 0 1 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 1 0 0 0 0 0 0 0 0 0
## X5267 X5268 X5269 X5270 X5271 X5272 X5273 X5274 X5275 X5276 X5277 X5278 X5279
## 1 0 0 0 0 1 0 0 0 0 1 0 0 0
## 2 0 0 0 0 0 0 0 0 0 1 0 0 0
## 3 0 0 0 0 0 0 0 0 0 1 0 0 0
## 4 0 0 0 0 1 0 0 0 0 0 0 0 0
## 5 0 0 0 0 1 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 1 0 0 0
## X5280 X5281 X5282 X5283 X5284 X5285 X5286 X5287 X5288 X5289 X5290 X5291 X5292
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 1 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5293 X5294 X5295 X5296 X5297 X5298 X5299 X5300 X5301 X5302 X5303 X5304 X5305
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5306 X5307 X5308 X5309 X5310 X5311 X5312 X5313 X5314 X5315 X5316 X5317 X5318
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5319 X5320 X5321 X5322 X5323 X5324 X5325 X5326 X5327 X5328 X5329 X5330 X5331
## 1 0 0 0 0 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0 0 0 0 0
## X5332 X5333 X5334 X5335 X5336 X5337 X5338 X5339 X5340
## 1 0 0 0 0 0 0 0 0 0
## 2 0 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0 0
## 4 0 0 0 0 0 0 0 0 0
## 5 0 0 0 0 0 0 0 0 0
## 6 0 0 0 0 0 0 0 0 0vcf_scaled[, -c(1:6)] <- scale(vcf_noNA[, -c(1:6)])vcf_pca <- prcomp(vcf_scaled[,-c(1:6)])##Save and Write Data ###For the final report
write.csv(vcf_scaled, file = "cleaned_data.csv", row.names = F)