prepare_dataset {OMICsPCA} | R Documentation |
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.
prepare_dataset(factdir, annofile, annolist, ...)
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()" |
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.
a dataframe of intersected values.
Subhadeep Das <subhadeep1024@gmail.com>
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)