defineBins: Define Bins

In Rcade: R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data

Description

Defines bins about the 5' end of certain features of interest - these features are usually transcripts.

Usage

defineBins(anno, zone, geneID="ensembl_gene_id", removeDuplicates=TRUE)

Arguments

anno	data.frame (or, an object that can be coerced to a data.frame, such as a GRanges) - Annotation information, corresponding to features of interest (usually transcripts). Only the 5' end of each object is used. Rcade expects the following column names: chr, start, end, str. These correspond to chromosome name, start co-ordinate, end co-ordinate and strand. Additionally, there must be another column specifying a gene ID, specified by the geneID argument.
zone	integer - must be a length 2 vector of form c(relative.start, relative.end). For example, zone = c(-10,100) will produce bins that start 10bp 5' of each transcript's TSS and end 100bp 3' of it.
geneID	character or integer - The column in anno that contains a geneID (or some other feature ID).
removeDuplicates	logical - If TRUE, then any rows that share the same geneID and genomic location as another row will be removed (even if any of the other columns are different).

Details

The defineBins function is useful when ChIP-seq bins are defined about ... . In particular, biomaRt data can be fed into this function directly. FIXME See vignette.

Value

A GRanges object, corresponding to genomic bins. This output can be used as the ChIPannoZones argument in RcadeAnalysis.

Author(s)

Jonathan Cairns

See Also

RcadeAnalysis

Examples

## Not run: 	##acquire annotation from biomaRt
	library(biomaRt)
	anno <- getBM(
		attributes= c("ensembl_gene_id", "chromosome_name",
			"transcript_start", "transcript_end", "strand"),
		mart= useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
	)

## End(Not run)
#define bins about the annotation
anno <- anno[order(anno$chromosome_name),]
colnames(anno) <- c("ENSG","chr","start","end","str")
ChIPannoZones <- defineBins(anno, c(-1500, 1500), geneID = "ENSG")

Rcade documentation built on Nov. 8, 2020, 6:25 p.m.