suppa.get.final.table: Combine dpis, psi and tpm file together I modified the code...

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

Combine dpis, psi and tpm file together I modified the code from https://github.com/comprna/SUPPA/blob/master/scripts/Volcano_MA_plot.R

Description

Combine dpis, psi and tpm file together I modified the code from https://github.com/comprna/SUPPA/blob/master/scripts/Volcano_MA_plot.R

Usage

suppa.get.final.table(
  sample.names = "",
  psi = "",
  dpsi = "",
  event.tpm = "",
  pval.cutoff = 0.05,
  dpsi.cutoff = 0.3,
  tpm.cutoff = 0
)

Arguments

sample.names	A vector specify the column name of each psi in psivec file.
psi	Psivec file. Generate by Suppa2 diffSplice
dpsi	Dpsi file. Generate by Suppa2 diffSplice file
event.tpm	Event TPM file. Should be specified in Suppa analysis by –save_tpm_events
pval.cutoff	P-value cutoff
dpsi.cutoff	ΔPSI cutoff
tpm.cutoff	Mean TPM cutoff

Value

A data.frame

Examples

suppa.get.final.table(sample.names = smp.names,
         dpsi = "analysis/05suppa/diffSplice.events.dpsi.temp.0",
         psi  = "analysis/05suppa/diffSplice.events.psivec",
         event.tpm = "analysis/05suppa/diffSplice.events_avglogtpm.tab",
         dpsi.cutoff = dpsi.cutoff, pval.cutoff = pval.cutoff, tpm.cutoff = tpm.cutoff)

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.