peak_join: Integrate H3K4me3 data and Pol II data.

In ipumin/primirTSS: Prediction of pri-miRNA Transcription Start Site

Description

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.

Usage

peak_join(peak1, peak2)

Arguments

peak1	H3K4me3 peaks. Merged peak data as GRange object by fucntion peak_merge
peak2	Pol II peaks. Merged peak data as GRange object by fucntion peak_merge

Value

A GRanges object. The joined peaks for the following analysis to search for TSSs.

Detail

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.

Examples

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)

ipumin/primirTSS documentation built on June 10, 2020, 9:52 a.m.