readCufflinksFiles: reads cufflinks output Files

In psikon/cuffgo: cufflinks and GO analysis

Description

This wrapper function parses the output files generated by the programs cufflinks, cuffcompare, cuffmerge and cuffdiff and generates a dataframe with all containing data

Usage

         readCufflinksFiles(filename, program = "cufflinks")
         

Arguments

filename	path of the output file
program	output of which program have to be parsed (default="cufflinks")

Details

the following files can be parsed with this function:

transcripts.gtf

This GTF file contains Cufflinks' assembled isoforms

<outprefix>.combined.gtf

Cuffcompare reports a GTF file containing the "union" of all transfrags in each sample.

<outprefix>/merged.gtf

cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies.

isoform_exp.diff

Transcript differential FPKM

gene_exp.diff

Gene differential FPKM. Tests differences in the summed FPKM of transcripts sharing each gene_id

tss_group_exp.diff

Primary transcript differential FPKM. Tests differences in the summed FPKM of transcripts sharing each tss_id

cds_exp.diff

Coding sequence differential FPKM. Tests differences in the summed FPKM of transcripts sharing each p_id independent of tss_id

Value

dataframe

content of the Input file as dataframe

References

Cufflinks Manual:http://cufflinks.cbcb.umd.edu/manual.html

Examples

         ## read cufflinks GTF File
         readCufflinksFiles(system.file("extdata","cufflinks.gtf",package="cuffGO"),"cufflinks")
         
         ## read cuffmerge GTF File
         readCufflinksFiles(system.file("extdata","cuffmerge.gtf",package="cuffGO"),"cuffmerge")
      
         ##read cuffcompare GTF File
         readCufflinksFiles(system.file("extdata","cuffcompare.gtf",package="cuffGO"),"cuffcompare")
         
         ## read cuffdiff File
         readCufflinksFiles(system.file("extdata","cuffdiff.diff",package="cuffGO"),"cuffdiff")
         

psikon/cuffgo documentation built on May 26, 2019, 10:32 a.m.