csaw (version 1.6.1)

Parameter list methods: Get or modify readParam lists

Description

Extract and modify lists of library-specific readParam objects

Usage

reformList(paramlist, ...)
checkList(paramlist)

Arguments

paramlist

a list of readParam objects

...

other arguments, to be passed to reform

Value

For reformList, a list of library-specific readParam objects is returned.For checkList, a character vector is returned containing all non-identical parameters across the list.

Details

The reformList function sets the parameters specified in ... across all elements of paramlist. This standardizes all of the internal readParam objects, e.g., for the restrict parameter. If paramlist is a single readParam object, then reformList is equivalent to reform.

The checkList function checks which parameter settings are identical between elements of paramlist. This is useful when some parameters must be variable, while others must be the same.

See Also

windowCounts, regionCounts, reform

Examples

bamFiles <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
data <- windowCounts(bamFiles, width=100, filter=1)
data$param

data <- windowCounts(bamFiles, width=100, filter=1, param=list(readParam(), readParam(minq=100)))
data$param
data[,1]$param
data[,2]$param

plist <- data$param
reformList(plist, restrict="chrA")
reformList(plist, minq=10)

checkList(plist)
checkList(reformList(plist, minq=10))