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]