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2.9 years ago
Cody
•
0
I am trying to summarize quant.sf files from 9 samples. I am trying to follow this vignette (https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html).
My quant.sf files are in 9 different sample files in a directory named 'Salmon'.
I created a vector of file names by:
> samples <- read.table(file.path(dir, "samples.txt"), header = TRUE)
> samples
files group_name names
1 sample_1_S1_R1_001.trim.fastq Air Air_1
2 sample_2_S2_R1_001.trim.fastq Air Air_2
3 sample_3_S3_R1_001.trim.fastq Air Air_3
4 sample_4_S4_R1_001.trim.fastq O3_24hr 24_1
5 sample_5_S5_R1_001.trim.fastq O3_24hr 24_2
6 sample_6_S6_R1_001.trim.fastq O3_24hr 24_3
7 sample_7_S7_R1_001.trim.fastq O3_72hr 72_1
8 sample_8_S8_R1_001.trim.fastq O3_72hr 72_2
9 sample_9_S9_R1_001.trim.fastq O3_72hr 72_3
I tried pointing to the files by:
> files <- c("/scratch/lcs152/transcripts_quant/salmon/sample_1_S1_R1_001.trim.fastq/quant.sf", "/scratch/lcs152/transcripts_quant/salmon/sample_2_S2_R1_001.trim.fastq/quant.sf", "/scratch/lcs152/transcripts_quant/salmon/sample_3_S3_R1_001.trim.fastq/quant.sf", "/scratch/lcs152/transcripts_quant/salmon/sample_4_S4_R1_001.trim.fastq/quant.sf", "/scratch/lcs152/transcripts_quant/salmon/sample_5_S5_R1_001.trim.fastq/quant.sf", "/scratch/lcs152/transcripts_quant/salmon/sample_6_S6_R1_001.trim.fastq/quant.sf", "/scratch/lcs152/transcripts_quant/salmon/sample_7_S7_R1_001.trim.fastq/quant.sf", "/scratch/lcs152/transcripts_quant/salmon/sample_8_S8_R1_001.trim.fastq/quant.sf", "/scratch/lcs152/transcripts_quant/salmon/sample_9_S9_R1_001.trim.fastq/quant.sf")
Then adding names by:
>names(files) <- paste0(samples$name)
Then I checked to see the files were named properly:
> files
Air_1
"/scratch/lcs152/transcripts_quant/salmon/sample_1_S1_R1_001.trim.fastq/quant.sf"
Air_2
"/scratch/lcs152/transcripts_quant/salmon/sample_2_S2_R1_001.trim.fastq/quant.sf"
Air_3
"/scratch/lcs152/transcripts_quant/salmon/sample_3_S3_R1_001.trim.fastq/quant.sf"
24_1
"/scratch/lcs152/transcripts_quant/salmon/sample_4_S4_R1_001.trim.fastq/quant.sf"
24_2
"/scratch/lcs152/transcripts_quant/salmon/sample_5_S5_R1_001.trim.fastq/quant.sf"
24_3
"/scratch/lcs152/transcripts_quant/salmon/sample_6_S6_R1_001.trim.fastq/quant.sf"
72_1
"/scratch/lcs152/transcripts_quant/salmon/sample_7_S7_R1_001.trim.fastq/quant.sf"
72_2
"/scratch/lcs152/transcripts_quant/salmon/sample_8_S8_R1_001.trim.fastq/quant.sf"
72_3
"/scratch/lcs152/transcripts_quant/salmon/sample_9_S9_R1_001.trim.fastq/quant.sf"
But when I check to see if they exist, it tells me they don't:
> all(file.exists(files))
[1] FALSE
I'm very much a novice and not sure if the information I've provided is helpful. Any guidance would be appreciated!
You may want to completely automate the file list creation using
list.files()
and apply:Do not delete posts that have received feedback.