NAs introduced by coercion

[Алексей Баринов]

Hello dear developers. 

I have moved to another virtual machine and faced problem  :

In segment(Y_qc, Yhat, optK = optK, K = K, sampname_qc, ref_qc,  :

  NAs introduced by coercion

BRCAyearmonth_chr17_2_CODEX_frac.txt has NA in chr name column. 

Could you please help to fix ? 

My R script is 

##source("/home/ubuntu/a.R")

library(CODEX)

dirPath <- "/home/ubuntu/data/"

bamFile <- list.files(dirPath, pattern = '*.bam$')

bamdir <- file.path(dirPath, bamFile)

sampname <- as.matrix(read.table(file.path(dirPath, "sampname")))

bedFile <- file.path(dirPath, "/targets/QIASEQBRCAPLUS.BED")

chrlist <- c("chr10","chr13","chr16","chr17")

for (i in chrlist)

{ i-> chr

bambedObj <- getbambed(bamdir = bamdir, bedFile = bedFile, 

                       sampname = sampname, projectname = "BRCAyearmonth", chr)

bamdir <- bambedObj$bamdir; sampname <- bambedObj$sampname

ref <- bambedObj$ref; projectname <- bambedObj$projectname; chr <- bambedObj$chr

coverageObj <- getcoverage(bambedObj, mapqthres = 20)

Y <- coverageObj$Y; readlength <- coverageObj$readlength

gc <- getgc(chr, ref)

mapp <- getmapp(chr, ref)

##leithtrash=20-2000

##K=1:9

qcObj <- qc(Y, sampname, chr, ref, mapp, gc, cov_thresh = c(100, 10000), 

    length_thresh = c(20, 3000), mapp_thresh = 0.8, gc_thresh = c(20, 80))

Y_qc <- qcObj$Y_qc; sampname_qc <- qcObj$sampname_qc; gc_qc <- qcObj$gc_qc

mapp_qc <- qcObj$mapp_qc; ref_qc <- qcObj$ref_qc; qcmat <- qcObj$qcmat

write.table(qcmat, file = paste(projectname, '_', chr, '_qcmat', '.txt', sep=''),

            sep='\t', quote=FALSE, row.names=FALSE)

normObj <- normalize(Y_qc, gc_qc, K = 1:9)

#normObj <- normalize2(Y_qc, gc_qc, K = 1:2, normal_index=c(1,3))

Yhat <- normObj$Yhat; AIC <- normObj$AIC; BIC <- normObj$BIC

RSS <- normObj$RSS; K <- normObj$K

choiceofK(AIC, BIC, RSS, K, filename = paste(projectname, "_", chr, 

"_choiceofK", ".pdf", sep = ""))

filename <- paste(projectname, "_", chr,".pdf", sep = "")

Kmax <- length(AIC)

par(mfrow = c(1, 3))

plot(K, RSS, type = "b", xlab = "Number of latent variables")

plot(K, AIC, type = "b", xlab = "Number of latent variables")

plot(K, BIC, type = "b", xlab = "Number of latent variables")

optK = K[which.max(BIC)]

finalcall <- segment(Y_qc, Yhat, optK = optK, K = K, sampname_qc,

    ref_qc, chr, lmax = 200, mode = "integer")

finalcall

write.table(finalcall, file = paste(projectname, '_', chr, '_', optK,

'_CODEX_frac.txt', sep=''), sep='\t', quote=FALSE, row.names=FALSE)

save.image(file = paste(projectname, '_', chr, '_image', '.rda', sep=''),

compress='xz')

}