defineBins {Rcade} | R Documentation |
Defines bins about the 5' end of certain features of interest - these features are usually transcripts.
defineBins(anno, zone, geneID="ensembl_gene_id", removeDuplicates=TRUE)
anno |
Rcade expects the following column names: |
zone |
|
geneID |
|
removeDuplicates |
|
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.
A GRanges
object, corresponding to genomic bins. This output can be used as the ChIPannoZones
argument in RcadeAnalysis
.
Jonathan Cairns
## 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")