prepare_dataset {OMICsPCA}R Documentation

Intersects and merge data from multiple experiments into a dataframe

Description

This function intersects feature files (e.g. ChIP-seq, RNA seq) with annotation files(e.g.exons, genes) and represents the intersected values of each annotation from all cell lines in a data frame.

Usage

prepare_dataset(factdir, annofile, annolist, ...)

Arguments

factdir

Full path of directory containing (only) feature (e.g ChIP-seq, CAGE) files in bed format

annofile

Full path of the annotation file (e.g. TSS, exon, gene) in bed format

annolist

Full path of the file containing name of the annotations (e.g. name of exons)

...

additional arguments to pass to "R_bedtools_intersect()" through "intersect()"

Details

If an annotation (e.g. gene) does not present in an assay file (e.g ChIP-seq of H3k9ac in the Cell Gm12878), this function puts a 0 as its value.

Value

a dataframe of intersected values.

Author(s)

Subhadeep Das <subhadeep1024@gmail.com>

Examples


anno <- system.file("extdata/annotation2/TSS_groups.bed",
                    package = "OMICsPCAdata")

list <- system.file("extdata/annotation2/TSS_list",
                    package = "OMICsPCAdata")

fact <- system.file("extdata/factors2/demofactor",
                    package = "OMICsPCAdata")

prepare_dataset(factdir = fact, annofile = anno, annolist = list)


[Package OMICsPCA version 1.10.0 Index]