Question: RAPIDR problem, I need anyone who can help me!
0
gravatar for martyferr90
2.0 years ago by
martyferr9030
martyferr9030 wrote:

Hi! I'm really desperate! I'm trying to use RAPIDR package, but I receive always this error:

    No outcomes for Sample 001
    No outcomes for Sample 003
    Error in `[.data.frame`(sampleIDs.with.outcomes, , "Gender") : 
    undefined columns selected

but I follow literally the tutorial! I work with ION Torrent bam but for align problem I used FASTQ file, I aligned with bowtie2 and sorted and indexed with samtools.

Is there anyone who use this package and can help me? I really need it!

nipt rapidr R • 757 views
ADD COMMENTlink modified 8 months ago by greeshmathulasi10 • written 2.0 years ago by martyferr9030
1

Your code, expected output and some example input data would be helpful in understanding the problem.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by cpad011212k

I am also getting same error as above:

Loading binned counts file
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

My code is

source("https://bioconductor.org/biocLite.R")
biocLite("SummarizedExperiment")
library(SummarizedExperiment)
makeBinnedCountsFile(bam.file.list = c("Sample1.bam","Sample2.bam","Sample3.bam","Sample4.bam"),
  sampleIDs = c("Sample1","Sample2","Sample3","Sample4"),  
  binned.counts.fname = "Rapidr-output",
  k = 20000)                  
library(RAPIDR)
rapidr.dir <- system.file(package = "RAPIDR")
data(outcomes)
data(gcContent)
T21.pos <- which(finalref$Dx == "T21")
chr.lens <- sapply(gcContent, length)
chr.names <- names(chr.lens)
header <- c("SampleID")
for (i in 1:length(chr.lens)) {
  header <- c(header, rep(chr.names[i], chr.lens[i]))  
}  
nbins <- sum(chr.lens)
ncols <- nbins + 1
binned.counts <- matrix(nrow = nrow(finalref), ncol = ncols)
for (i in 1:nrow(binned.counts)) {
  binned.counts[i,] <- rpois(ncols, lambda = 100)  
  if (i %in% T21.pos) {  
    binned.counts[i, 139087:141493] <- rpois(chr.lens[21], lambda = 115)    
  }
}    
binned.counts[,1] <- finalref$sampleID
colnames(binned.counts) <- header
t <- tempfile()
write.table(binned.counts, file = t, col.names = TRUE, row.names = FALSE, quote = FALSE, sep = ",")
"Rapidr-output" <- t
message(t)  
gcContent.fname <- paste(rapidr.dir, "C:/Users/Pooja/Documents/R/win-library/3.4/RAPIDR/data/gcContent.rda", sep = "")
head(outcomes)
ref.set <- createReferenceSetFromCounts("Rapidr-output",
                                        outcomes,                                        
                                        gcCorrect = FALSE,                                        
                                        PCA = FALSE,                                        
                                        filterBin = FALSE,                                        
                                        gcContentFile = gcContent.fname)  


**My input is**
outcomes
     sampleID.Gender.Dx
1 sample1,Female,Normal
2 sample2,Female,Normal
3   sample3,Male,Normal
4   sample4,Male,Normal

My session info is :

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252    LC_MONETARY=English_India.1252
[4] LC_NUMERIC=C                   LC_TIME=English_India.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] SummarizedExperiment_1.8.1        DelayedArray_0.4.1                matrixStats_0.53.1               
 [4] Biobase_2.38.0                    BiocInstaller_1.28.0              BSgenome.Hsapiens.UCSC.hg19_1.4.0
 [7] BSgenome_1.46.0                   rtracklayer_1.38.3                Biostrings_2.46.0                
[10] XVector_0.18.0                    GenomicRanges_1.30.3              GenomeInfoDb_1.14.0              
[13] IRanges_2.12.0                    S4Vectors_0.16.0                  BiocGenerics_0.24.0              
[16] RAPIDR_0.1.1                      NIPTeR_1.0.2                     

loaded via a namespace (and not attached):
 [1] zlibbioc_1.24.0          GenomicAlignments_1.14.2 BiocParallel_1.12.0      lattice_0.20-35         
 [5] tools_3.4.1              grid_3.4.1               data.table_1.11.2        Matrix_1.2-10           
 [9] GenomeInfoDbData_1.0.0   PropCIs_0.3-0            sets_1.0-18              bitops_1.0-6            
[13] RCurl_1.95-4.10          compiler_3.4.1           Rsamtools_1.30.0         XML_3.98-1.11
ADD REPLYlink modified 18 months ago by genomax75k • written 18 months ago by pooja.solanki0
0
gravatar for greeshmathulasi1
8 months ago by
greeshmathulasi10 wrote:

Hi Sorry for replying late. I hope this may useful... Change your input 'outcomes' as, SampleID Dx Gender sample1 Normal Female sample2 Normal Female sample3 Normal Male sample4 Normal Male

Thanks & Regards, Greeshma Thulasi

ADD COMMENTlink written 8 months ago by greeshmathulasi10
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