peak_join {primirTSS} | R Documentation

## Integrate H3K4me3 data and Pol II data.

### 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)

[Package primirTSS version 1.6.1 Index]