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

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Add metadata of the GRanges objects used for findOverlapsOfPeaks

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)

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.