score.filter: Filtering the scores for isoform switch

In wyguo/TSIS: Time-series isoform switch of alternative splicing

Filtering the scores for isoform switch

Description

Filtering the scores output from iso.switch.

Usage

score.filter(scores, prob.cutoff = 0.5, diff.cutoff = 1,
  t.points.cutoff = 2, pval.cutoff = 0.01, cor.cutoff = 0.5,
  data.exp = NULL, mapping = NULL, sub.isoform.list = NULL,
  sub.isoform = F, max.ratio = F, x.value.limit = c(9, 17))

Arguments

scores	the scores object output from iso.switch.
prob.cutoff, diff.cutoff, t.points.cutoff, pval.cutoff, cor.cutoff	the cut-offs corresponding to switch frequencies/probablities, sum of average sample differences, p-value and time points cut-offs for both intervals before and after switch and Pearson correlation.
data.exp, mapping	the expression and gene-isoform mapping data.
sub.isoform.list	a vector of isoforms to output the corresponding results (see TSIS.data$sub.isoforms).
sub.isoform	logical, to output subset of the results(TRUE) or not (FALSE). If TRUE, sub.isoform.list must be provided.
max.ratio	logical, to show maximum abundant isoform results(TRUE) or not (FALSE). If TRUE, data.exp and mapping data must be provided to calculate the isoform ratios to the genes using rowratio.
x.value.limit	the region of x axis (time) for investigation.

Details

Users can set cut-offs, such as for the probability/frequency of switch and sum of average differences, to further refine the switch results.

Value

a table of scores after filtering.

wyguo/TSIS documentation built on May 21, 2023, 12:36 a.m.