mergeResults: Wrappers to get region-level results

In LTLA/csaw: ChIP-Seq Analysis with Windows

Wrappers to get region-level results

Description

Convenience wrappers around lower-level functions to easily obtain region-level results from window statistics.

Usage

mergeResults(ranges, tab=mcols(ranges), tol, get.best=TRUE, 
    merge.args=list(), combine.args=list(), best.args=list())

overlapResults(ranges, tab=mcols(ranges), regions, get.best=TRUE, 
    overlap.args=list(), combine.args=list(), best.args=list())

Arguments

ranges	A GRanges or RangedSummarizedExperiment containing genomic intervals, usually for windows.
tab	A data.frame of differential binding results with one row per interval in ranges, to be passed to combineTests or combineOverlaps.
tol	A numeric scalar to be passed to mergeWindows.
get.best	A logical scalar indicating whether getBestTest or getBestOverlaps should be run.
regions	A GRanges class containing reference regions to overlap with the windows.
merge.args	Further arguments to pass to mergeWindows.
overlap.args	Further arguments to pass to findOverlaps.
combine.args	Further arguments to pass to combineTests or combineOverlaps.
best.args	Further arguments to pass to getBestTest or getBestOverlaps.

Details

mergeResults simply calls mergeWindows to identify clusters of windows corresponding to regions. These clusters are used in combineTests and (optionally) getBestTest to obtain per-region statistics.

overlapResults simply calls findOverlaps to identify all windows overlapping each reference region. These overlaps are used in combineOverlaps and (optionally) getBestOverlaps, where each set of overlapping windows for a reference region are used to define the latter's statistics.

These wrapper functions are simply for convenience. No other work is performed and so users are free to call the individual functions separately.

Value

mergeResults will return a DataFrame containing regions, the GRanges generated by clustering windows into regions; combined, the DataFrame containing combined statistics for each clustered region; and best, the DataFrame containing statistics for the best window in each clustered region. The metadata contains ids, an integer vector of cluster IDs for ranges from mergeWindows.

overlapResults will return a DataFrame containing regions, the same as the input GRanges of the same name; combined, the DataFrame containing combined statistics for each reference region; and best, the DataFrame containing statistics for the best window in each reference region. The metadata contains overlaps, a Hits object specifying the overlaps from findOverlaps.

Author(s)

Aaron Lun

See Also

mergeWindows, combineTests and getBestTest, for the functions that actually do the work in mergeResults.

findOverlaps, combineOverlaps and getBestOverlaps, for the functions that actually do the work in overlapResults.

Examples

# Making up some data.
tab <- data.frame(logFC=rnorm(20), logCPM=rnorm(20), PValue=rbeta(20, 1, 2))
gr <- GRanges("chrA", IRanges(sample(1000, 20), width=40))

# Merging windows.
(merge.out <- mergeResults(gr, tab, tol=1))
merge.out$merged
merge.out$combined

# Overlapping windows with a reference region.
regions <- GRanges("chrA", IRanges(c(10, 500, 900), width=20))
(olap.out <- overlapResults(gr, tab, regions=regions))
olap.out$regions
olap.out$combined

LTLA/csaw documentation built on Dec. 11, 2023, 5:11 a.m.