prepare_dataset: Intersects and merge data from multiple experiments into a...

In OMICsPCA: An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

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 <[e-mail]>

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)

OMICsPCA documentation built on Nov. 8, 2020, 5:01 p.m.