How can I export featureCounts (Rsubread) results?

Question

[gustavoborin01]

Hi everyone,

I'm trying to export the featureCounts output results of Rsubread to a .xls format (excel), but I'm not having success. I have got the counts of the reads from my RNASeq experiment, but I can't export the result. I used the command below, but it did not work. It appears that warning message.

I know the reportReads argument saves my output, but the generated files are so big and I know that exists a different and simpler way to do that. So, really appreciate if someone could help me.

Used function

> featureCounts(file="T_reesei_F24-2_GTGGCC_L008_R1_001.cleanreads.fastq.gz_tophat2/F24h-2_accepted_hits.bam",
  annot.ext = "TrireRUTC30_1_GeneCatalog_genes_20110526.fix2.gtf",
  isGTFAnnotationFile = TRUE,
  GTF.featureType = "CDS",
  GTF.attrType = "transcript_id")

Output results

1664                                         +;+;+   3186
1665                                           +;+    234
1666                                             +   1362
 [ reached getOption("max.print") -- omitted 8186 rows ]

$targets
[1] "T_reesei_F24.2_GTGGCC_L008_R1_001.cleanreads.fastq.gz_tophat2.F24h.2_accepted_hits.bam"

$stat
                      Status
1                   Assigned
2       Unassigned_Ambiguity
3    Unassigned_MultiMapping
4      Unassigned_NoFeatures
5        Unassigned_Unmapped
6  Unassigned_MappingQuality
7 Unassigned_FragementLength
8         Unassigned_Chimera
  T_reesei_F24.2_GTGGCC_L008_R1_001.cleanreads.fastq.gz_tophat2.F24h.2_accepted_hits.bam
1                                                                               34914980
2                                                                                   8021
3                                                                                  88386
4                                                                               11354142
5                                                                                      0
6                                                                                      0
7                                                                                      0
8                                                                                      0

Used command to export

> res <- write.table(res$table, file = "F24.xls")

Warning message

Error in res$counts : object of type 'closure' is not subsettable

Thanks
Gustavo Borin

Answer 1

[gustavoborin01]

For who had similar or the same problem like me, I found two successfully answers in another forum!

---

First option by James W. MacDonald

You have to capture the output of featureCounts(), by assigning it to an object.

counts <- featureCounts(<arguments go here>)

Then if you look at the help for featureCounts, you will see this:

Value:

     A list with the following components:

  counts: a data matrix containing read counts for each feature or
          meta-feature for each library.

And you can write that out to a file.

---

Second option by Wei Shi

Dear Gustavo Borin,

The 'reportReads' argument enables the detailed read assignment results to be saved into a file. The file includes overlapping features and other data for each read (each row corresponds a read). But I don't think that is what you want.

To save read counts generated from featureCounts, try the following command:

fc <- featureCounts(
  file="T_reesei_F24-2_GTGGCC_L008_R1_001.cleanreads.fastq.gz_tophat2/F24h-2_accepted_hits.bam",
  annot.ext="TrireRUTC30_1_GeneCatalog_genes_20110526.fix2.gtf",
  isGTFAnnotationFile = TRUE,
  GTF.featureType = "CDS",
  GTF.attrType = "transcript_id")

write.table(
  x=data.frame(fc$annotation[,c("GeneID","Length")],
    fc$counts,
    stringsAsFactors=FALSE),
  file="counts.txt",
  quote=FALSE,
  sep="\t",
  row.names=FALSE)

The generated 'counts.txt' file is a tab-delimited file which includes gene identifier, gene length and counts for each gene in each library.

Hope this helps.

Wei

[sivaranjanisk]

thanks, Wei Shi! your option worked for me