Question: RAPIDR mask and build the reference
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gravatar for martyferr90
6 days ago by
martyferr9020
martyferr9020 wrote:

Hi all! I'm new to RAPIDR usage and i have some problems.

First of all I would to know how I can obtain a mask bed file to perform the makeBinnedCountsFile with the mask.

The second question is: I'm trying to build a reference and using the code on the exemple (demo file in the package), but I receive this error:

Checking every sampleID has an outcome
No outcomes for Sample Sample1
No outcomes for Sample Sample2
No outcomes for Sample Sample3
No outcomes for Sample Sample4
Error in `[.data.frame`(sampleIDs.with.outcomes, , "Gender") : 
  undefined columns selected

and my code is:

> data(outcomes) 
> data(gcContent)
> T21.pos <- which(outcomes$Dx == "T21") 
> chr.lens <- sapply(gcContent, length)
> chr.names <- names(chr.lens) 
> header <- c("SampleID") 
> for (i in 1:length(chr.lens)) { 
+    header <- c(header, rep(chr.names[i], chr.lens[i]))
+ }
> nbins <- sum(chr.lens)
> ncols <- nbins + 1 
> 
> binned.counts <- matrix(nrow = nrow(outcomes), ncol = ncols) 
> for (i in 1:nrow(binned.counts)) { 
+    binned.counts[i,] <- rpois(ncols, lambda = 100) 
+    if (i %in% T21.pos) {
+       binned.counts[i, 139087:141493] <- rpois(chr.lens[21], lambda = 115) 
+    }
+ }
> binned.counts[,1] <- outcomes$SampleID 
> colnames(binned.counts) <- header 
> t <- tempfile()
> write.table(binned.counts, file = t, col.names = TRUE, row.names = FALSE, quote = FALSE, sep = ",") 
> 
> "mybinnedfile.fname" <- t
> message(t)
> rapidr.dir <- system.file(pakage = "RAPIDR")
> gcContent.fname <- paste(rapidr.dir, "data/gcContent.RData", sep="")
> head(outcomes)
  SampleID     Dx Gender
1     1000 Normal Female
2     1001 Normal Female
3     1002    T21 Female
4     1003 Normal   Male
5     1004 Normal   Male
6     1005 Normal   Male
> ref.set  <- createReferenceSetFromCounts("mybinnedfile.fname", outcomes, gcCorrect = FALSE, PCA = FALSE, method = "NCV")

Where I'm wrong? Is it normal that the outcomes has 9 sample whilst I loaded only 4 sample?

nipt rapdir bam ngs R • 119 views
ADD COMMENTlink written 6 days ago by martyferr9020
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