newIntronRetention: Compute intron retention

Description Usage Arguments Value

View source: R/IntronRetention.R

Description

Create an IntronRetention object.

Usage

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newIntronRetention(targetExpression, intronToUnion, groups,
  unique_counts = NULL, psi = TRUE)

Arguments

targetExpression

a matrix of nothing but expression values and one column containing 'target_id's

intronToUnion

a table with columns (all character vectors):

intron

the identifier of the intron

target_id

the target_id of transcripts compatible with the intron

gene

the gene name that this intron belongs to

intron_extension

the actual coordinates of the intron quantified (including the region that overlaps the intronic region)

groups

a vector with the grouping

psi

if TRUE, compute the psi value. otherwise, compute a rate

Value

an IntronRetention object


pachterlab/kma documentation built on May 24, 2019, 5:58 p.m.