rasp: rasp

In isglobal-brge/rasp: Differential alternative splicing test.

Description

Differential alternative splicing test.

Usage

rasp(
  formula,
  x,
  group,
  expressionCols,
  geneidCol,
  filterInd = 0.1,
  filterExon = 0.05,
  transform = "none",
  cores = 1,
  ...
)

Arguments

formula	a 'formula' with a symbolic description of the model to be fitted.
x	expression dataset. Can be of class 'DEXSeqDataSet', 'SummarizedExperiment' or 'RangedSummarizedExperiment'. A 'matrix' or 'data.frame' is also accepted.
group	a 'factor' representing the condition of each individual. Required if 'x' is a 'matrix' or 'data.fame', ignored otherwise.
expressionCols	'character' or 'numeric' vector specifying the columns of 'x' with that contain the expression data (i.e. the different samples). Required if 'x' is a 'matrix' or 'data.fame', ignored otherwise.
geneidCol	name or index of the column of 'x' encoding the gene IDs. Required if 'x' is a 'matrix' or 'data.fame', ignored otherwise.
filterInd	filter individuals (samples) with mean relative frequency < 'filterInd'.
filterExon	filter exons with mean relative frequency < 'filterFreq'.
transform	argument for 'mlm'. Can be any of 'none', 'sqrt' or 'log'.
cores	'integer'. Number of parallel processes to use.
...	additional arguments passed to 'mlm'.

Details

Test for differential alternative splicing across two or more conditions.

Value

A 'rasp' class 'matrix' containing the p-values (also adjusted for multiple testing). 'NA' will be returned for single exon genes and genes not passing filtering criteria.

Examples

data(adipose)
rasp(~ inv16p11.2, adipose.chr16)

data("YRI")
rasp(x = YRI, group = attr(YRI, "gender"), expressionCols = 3:71, geneidCol = "gene_id")

isglobal-brge/rasp documentation built on July 12, 2020, 1:17 a.m.