parseChIP: parseChIP

In umbibio/CIE-R-Package: Causal Inference and Directional Enrichment Methods on Biological Networks

parseChIP

Description

Process unfiltered ChIP Atlas data, pulled into a folder with a script like the one that can be found in ../inst/shellScripts/. Can either return a list of data frames suitable for filtering with filterChIPAtlas (regardless of species) or .rels and .ents tables suitable for running enrichment or other purposes.

Usage

parseChIP(tsv_dir, processToFilterLater=FALSE)

Arguments

tsv_dir	The directory containing the data pulled from ChIP Atlas.
processToFilterLater	A switch controlling whether the output will be .ents and .rels tables (FALSE) or a list of data frames suitable for later filtering by filterChIPAtlas (TRUE). Defaults to FALSE

Value

A list of two data frames (ents and rels) or a list of dataframes suitable for later processing.

Examples

## Both these examples assume you pulled the ChIP Atlas data
## and it can be found at the location "../data/chip-atlas-10kb/"

## Example One
chip-atlas-10kb <- parseChIP("../data/chip-atlas-10kb/",
                             processToFilterLater=TRUE)
saveRDS(chip-atlas-10kb, "../data/chip-atlas-10kb.rds")

entsRels <- filterChIPAtlas(10, 500, "average",
                            databaseDir="../data")
View(entsRels$filteredChIP.ents)
View(entsRels$filteredChIP.rels)

## Example Two

entsRels <- parseChIP("../data/chip-atlas-10kb/")
View(entsRels$ents)
View(entsRels$rels)

umbibio/CIE-R-Package documentation built on Sept. 26, 2023, 3:37 a.m.