Description Usage Arguments Value Detail Examples
Integrate peaks from H3K4me3 and Pol II data. To conduct the overlappd ranges for the further analysis by imposing H3K4me3 peaks on Pol II peaks, if both of these two different kinds of ChIP-seq data are available.
1 | peak_join(peak1, peak2)
|
peak1 |
H3K4me3 peaks. Merged peak data as |
peak2 |
Pol II peaks. Merged peak data as |
A GRanges object. The joined peaks for the following analysis to search for TSSs.
Peak1 and peak2 are signals seperately from the ChIP-seq
data of H3K4me3 and Pol II data that to be integrated. The data is
GRange
object containing three columns Chrom
, Ranges
,
Strand
. And the order of these two kinds of data when input as
peak1
and peak2
can be swapped.
1 2 3 4 5 6 7 8 9 10 11 12 13 | peak_df1 <- data.frame(chrom = c("chr1", "chr1", "chr1", "chr2"),
start = c(100, 460, 600, 70),
end = c(200, 500, 630, 100),
stringsAsFactors = FALSE)
peak1 <- as(peak_df1, "GRanges")
peak_df2 <- data.frame(chrom = c("chr1", "chr1", "chr1", "chr2"),
start = c(160, 470, 640, 71),
end = c(210, 480, 700, 90),
stringsAsFactors = FALSE)
peak2 <- as(peak_df2, "GRanges")
peak_join(peak1, peak2)
|
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