find_switches: Find isoform switches

In hclimente/scudo: Switch Catcher, Uprooting Differentially-expressed Ones

Description

Find the isoform switches that match all of the following conditions: 1) genes are not differentially expressed; 2) abs(deltaPSI) is > 0.05 and more extreme than 1 involved transcripts are sufficiently expressed (TPM > 0.1).

Usage

find_switches(tx_pdPSI, gene_pDE, pDE = 0.01, pdPSI = 0.01,
  deltaPSI = 0.05, minExpression = 0.1)

Arguments

tx_pdPSI	data.frame with transcript-level annotation per sample, as outputted by score_delta. Must contain all of the following columns: dPSI indicating the deltaPSI and p scoring how extreme it is; tpmCtrl and tpmCase indicating the expression in the two conditions; and transcript, gene and sample.
gene_pDE	data.frame with gene-level annotation per sample, as outputted by score_delta. Must contain all of the following columns: p indicating if the gene is differentially expressed; and gene and sample.
pDE	Minimum p-value to consider a gene differentially expressed.
pdPSI	Minimum p-value to consider a scplicing change significant.
deltaPSI	Minimum PSI change to consider a scplicing change significant.
minExpression	Minimum expression of a transcript to consider it expressed.

Value

A data.frame with the measured isoform switches.

hclimente/scudo documentation built on May 25, 2019, 5:26 p.m.