subset: subset ballgown objects to specific samples or genomic...

In alyssafrazee/ballgown-release: Flexible, isoform-level differential expression analysis

Description

subset ballgown objects to specific samples or genomic locations

Usage

subset(x, ...)

## S4 method for signature 'ballgown'
subset(x, cond, genomesubset = TRUE)

Arguments

x	a ballgown object
...	further arguments to generic subset
cond	Condition on which to subset. See details.
genomesubset	if TRUE, subset x to a specific part of the genome. Otherwise, subset x to only include specific samples. TRUE by default.

Details

To use subset, you must provide the cond argument as a string representing a logical expression specifying your desired subset. The subset expression can either involve column names of texpr(x, "all") (if genomesubset is TRUE) or of pData(x) (if genomesubset is FALSE). For example, if you wanted a ballgown object for only chromosome 22, you might call subset(x, "chr == 'chr22'"). (Be sure to handle quotes within character strings appropriately).

Value

a subsetted ballgown object, containing only the regions or samples satisfying cond.

Author(s)

Alyssa Frazee

Examples

data(bg)
bg_twogenes = subset(bg, "gene_id=='XLOC_000454' | gene_id=='XLOC_000024'")
bg_twogenes
# ballgown instance with 4 assembled transcripts and 20 samples

bg_group0 = subset(bg, "group == 0", genomesubset=FALSE)
bg_group0
# ballgown instance with 100 assembled transcripts and 10 samples

alyssafrazee/ballgown-release documentation built on May 12, 2019, 1:40 a.m.