Question

tximport allfile.exists(files)--> FALSE

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gilles.charpigny • 0

@gillescharpigny-16618

Last seen 5.7 years ago

Using "tximport package" I get the same error message reported 22 months ago by "ctl" but i am not able to resolve the problem with the Michael's answer.

When I specify all(file.exists(files)), I get FALSE. I even get this message with the tutorial command lines:

library(tximportData)
dir <- system.file("extdata", package ="tximportData")
list.files(dir)
samples <- read.table(file.path(dir, "samples.txt"), header = TRUE)
samples
files <- file.path(dir, "salmon", samples$run, "quant.sf.gz")
names(files) <- paste0("sample", 1:6) 
all(file.exists(files))

[1] FALSE

Where am I wrong?

Thank you very for your help

GCH

tximport • 2.4k views

ADD COMMENT • link updated 6.3 years ago by James W. MacDonald 67k • written 6.3 years ago by gilles.charpigny • 0

score 0 · Answer 1 · 2018-07-24

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 days ago

United States

You might have a borked installation of tximportData. Your code works for me:

 library(tximportData)
dir <- system.file("extdata", package ="tximportData")
list.files(dir)
samples <- read.table(file.path(dir, "samples.txt"), header = TRUE)
samples
files <- file.path(dir, "salmon", samples$run, "quant.sf.gz")
names(files) <- paste0("sample", 1:6)
all(file.exists(files))
library(tximportData)
> dir <- system.file("extdata", package ="tximportData")
> list.files(dir)
 [1] "cufflinks"               "derivedTxome"           
 [3] "kallisto"                "kallisto_boot"          
 [5] "rsem"                    "sailfish"               
 [7] "salmon"                  "salmon_gibbs"           
 [9] "samples.txt"             "samples_extended.txt"   
[11] "tx2gene.csv"             "tx2gene.gencode.v27.csv"
> samples <- read.table(file.path(dir, "samples.txt"), header = TRUE)
> samples
  pop center                assay    sample experiment       run
1 TSI  UNIGE NA20503.1.M_111124_5 ERS185497  ERX163094 ERR188297
2 TSI  UNIGE NA20504.1.M_111124_7 ERS185242  ERX162972 ERR188088
3 TSI  UNIGE NA20505.1.M_111124_6 ERS185048  ERX163009 ERR188329
4 TSI  UNIGE NA20507.1.M_111124_7 ERS185412  ERX163158 ERR188288
5 TSI  UNIGE NA20508.1.M_111124_2 ERS185362  ERX163159 ERR188021
6 TSI  UNIGE NA20514.1.M_111124_4 ERS185217  ERX163062 ERR188356
> files <- file.path(dir, "salmon", samples$run, "quant.sf.gz")
> names(files) <- paste0("sample", 1:6)
> all(file.exists(files))
[1] TRUE

What does your files object contain? Are there six files?

ADD COMMENT • link 6.3 years ago James W. MacDonald 67k

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I removed tximport/tximportData and reloaded.
The erreu code remains the same. Below is a copy of the output. I added a line to see the object file as requested.
(The version is R3.4.4)

> library(tximportData)
> dir <- system.file("extdata", package ="tximportData")
> list.files(dir)
 [1] "cufflinks"            "kallisto"             "kallisto_boot"        "rsem"                 "sailfish"            
 [6] "salmon"               "salmon_gibbs"         "samples.txt"          "samples_extended.txt" "tx2gene.csv"         
> samples <- read.table(file.path(dir, "samples.txt"), header = TRUE)
> samples
  pop center                assay    sample experiment       run
1 TSI  UNIGE NA20503.1.M_111124_5 ERS185497  ERX163094 ERR188297
2 TSI  UNIGE NA20504.1.M_111124_7 ERS185242  ERX162972 ERR188088
3 TSI  UNIGE NA20505.1.M_111124_6 ERS185048  ERX163009 ERR188329
4 TSI  UNIGE NA20507.1.M_111124_7 ERS185412  ERX163158 ERR188288
5 TSI  UNIGE NA20508.1.M_111124_2 ERS185362  ERX163159 ERR188021
6 TSI  UNIGE NA20514.1.M_111124_4 ERS185217  ERX163062 ERR188356
> files <- file.path(dir, "salmon", samples$run, "quant.sf.gz")
> nameFile<-names(files) <- paste0("sample", 1:6)
> nameFile
[1] "sample1" "sample2" "sample3" "sample4" "sample5" "sample6"
> all(file.exists(files))
[1] FALSE

ADD REPLY • link 6.3 years ago gilles.charpigny • 0

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What do you get from

data.frame(thefiles = files, doihave = file.exists(files))
                                                                                        thefiles
sample1 C:/Users/aajm-mobile/R/win-library/3.5/tximportData/extdata/salmon/ERR188297/quant.sf.gz
sample2 C:/Users/aajm-mobile/R/win-library/3.5/tximportData/extdata/salmon/ERR188088/quant.sf.gz
sample3 C:/Users/aajm-mobile/R/win-library/3.5/tximportData/extdata/salmon/ERR188329/quant.sf.gz
sample4 C:/Users/aajm-mobile/R/win-library/3.5/tximportData/extdata/salmon/ERR188288/quant.sf.gz
sample5 C:/Users/aajm-mobile/R/win-library/3.5/tximportData/extdata/salmon/ERR188021/quant.sf.gz
sample6 C:/Users/aajm-mobile/R/win-library/3.5/tximportData/extdata/salmon/ERR188356/quant.sf.gz
        doihave
sample1    TRUE
sample2    TRUE
sample3    TRUE
sample4    TRUE
sample5    TRUE
sample6    TRUE

ADD REPLY • link 6.3 years ago James W. MacDonald 67k

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what i get

> data.frame(thefiles = files, doihave = file.exists(files))
                                                                                thefiles doihave
sample1 F:/Documents/R/win-library/3.4/tximportData/extdata/salmon/ERR188297/quant.sf.gz   FALSE
sample2 F:/Documents/R/win-library/3.4/tximportData/extdata/salmon/ERR188088/quant.sf.gz   FALSE
sample3 F:/Documents/R/win-library/3.4/tximportData/extdata/salmon/ERR188329/quant.sf.gz   FALSE
sample4 F:/Documents/R/win-library/3.4/tximportData/extdata/salmon/ERR188288/quant.sf.gz   FALSE
sample5 F:/Documents/R/win-library/3.4/tximportData/extdata/salmon/ERR188021/quant.sf.gz   FALSE
sample6 F:/Documents/R/win-library/3.4/tximportData/extdata/salmon/ERR188356/quant.sf.gz   FALSE

>

ADD REPLY • link 6.3 years ago gilles.charpigny • 0

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You have an old version of R and Bioconductor. On my old version I get FALSE for all as well, so you need to upgrade to R-3.5.x and the release version of Bioc

ADD REPLY • link 6.3 years ago James W. MacDonald 67k

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Thank you vry much.

I updated R to R3.5. with the latest release of Bioc and it's ok; I have now difficulties with tximport with Bovine database. I added another question on the forum.

ADD REPLY • link 6.3 years ago gilles.charpigny • 0