addMetadata: Add metadata of the GRanges objects used for...

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description

Add metadata to to overlapping peaks after calling findOverlapsOfPeaks.

Usage

addMetadata(ol, colNames = NULL, FUN = c, ...)

Arguments

ol	An object of overlappingPeaks, which is output of findOverlapsOfPeaks.
colNames	Names of metadata column to be added. If it is NULL, addMetadata will guess what to add.
FUN	A function to be called
...	Arguments to the function call.

Value

return value is An object of overlappingPeaks.

Author(s)

Jianhong Ou

See Also

See Also as findOverlapsOfPeaks

Examples

peaks1 <- GRanges(seqnames=c(6,6,6,6,5),
                 IRanges(start=c(1543200,1557200,1563000,1569800,167889600),
                         end=c(1555199,1560599,1565199,1573799,167893599),
                         names=c("p1","p2","p3","p4","p5")),
                 strand="+",
                 score=1:5, id=letters[1:5])
peaks2 <- GRanges(seqnames=c(6,6,6,6,5),
                  IRanges(start=c(1549800,1554400,1565000,1569400,167888600),
                          end=c(1550599,1560799,1565399,1571199,167888999),
                          names=c("f1","f2","f3","f4","f5")),
                  strand="+",
                  score=6:10, id=LETTERS[1:5])
ol <- findOverlapsOfPeaks(peaks1, peaks2)
addMetadata(ol)

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.