Question: Error in tximport: all(file.exists(files)) is not TRUE
0
gravatar for Farah
17 months ago by
Farah70
Farah70 wrote:

Hello,

I am importing kallisto output files into R through tximport package and then using DESeqDataSetFromTximport() funstion. I am following the DESeq2 tutorial (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html).

So, first to construct the tx2gene table for linking transcripts to genes, I did as below (based on Tximport vignette):

library(tximportData)
dir <- system.file("extdata", package = "tximportData")
list.files(dir)
tx2gene <- read_csv(file.path(dir, "tx2gene.gencode.v27.csv"))
Parsed with column specification:
cols(
  TXNAME = col_character(),
  GENEID = col_character()
)
#
  

Then, I did as below to read my meta data file:

datadir <- "/scratch/fs/ye/"
meta <- read.delim(paste0(datadir, "/ye_meta.txt"),
                   header = TRUE, as.is = TRUE)
rownames(meta) <- meta$names
meta$trt <- factor(meta$trt)
meta$cell <- factor(meta$cell)

Finally, to do tximport, I ran as follows, however, I got the below Error:

kallistofiles <- file.path(datadir,"/kallisto/", meta$names, ".*-abundance.tsv")
names(kallistofiles) <- meta$names
txi <- tximport(kallistofiles, type="kallisto", tx2gene=tx2gene)

Error in tximport(kallistofiles, type = "kallisto", tx2gene = tx2gene) : all(file.exists(files)) is not TRUE

So, I performed file.exists() as suggested in another post:

file.exists("tx2gene")
[1] FALSE
  
file.exists(kallistofiles)
[1] FALSE FALSE FALSE FALSE FALSE FALSE
  

However, when I only run kallistofiles, it can read my kallistofiles:

kallistofiles
                                                    SRR6822797
"/scratch/fs/ye///kallisto//SRR6822797/.*-abundance.tsv"
                                                    SRR6822798
"/scratch/fs/ye///kallisto//SRR6822798/.*-abundance.tsv"
                                                    SRR6822799
"/scratch/fs/ye///kallisto//SRR6822799/.*-abundance.tsv"
                                                    SRR6822800
"/scratch/fs/ye///kallisto//SRR6822800/.*-abundance.tsv"
                                                    SRR6822801
"/scratch/fs/ye///kallisto//SRR6822801/.*-abundance.tsv"
                                                    SRR6822802
"/scratch/fs/ye///kallisto//SRR6822802/.*-abundance.tsv"
  

I would highly appreciate if you can help me how to solve this Error. Thanks you so much.

deseq2 tximport • 2.0k views
ADD COMMENTlink modified 17 months ago by h.mon32k • written 17 months ago by Farah70
1

.*-abundance.tsv are not file names. What are the names of the files under each folder? You may use

list.files( "/scratch/fs/ye///kallisto//SRR6822802/" )

to check the names.

ADD REPLYlink written 17 months ago by h.mon32k

Thank you very much for your guide.

ADD REPLYlink written 17 months ago by Farah70
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