getAnnotations {chromVAR} | R Documentation |
getAnnotations
getAnnotations(annotations, ...) ## S4 method for signature 'GRangesList' getAnnotations(annotations, rowRanges, ...) ## S4 method for signature 'MatrixOrmatrix' getAnnotations(annotations, ...) ## S4 method for signature 'data.frame' getAnnotations(annotations, ...) ## S4 method for signature 'list' getAnnotations(annotations, npeaks = NULL, ...) ## S4 method for signature 'character' getAnnotations(annotations, rowRanges, column = NULL, ...)
annotations |
matrix, Matrix, or data.frame of fragment counts, or SummarizedExperiment with counts assays, see details |
... |
additional arguments to pass to SummarizedExperiment |
rowRanges |
GenomicRanges or GenomicRangesList or RangedSummarizedExperiment |
npeaks |
number of peaks |
column |
column of bed file with annotation names, see details |
SummarizedExperiment object with 'matches' assay
GRangesList
: get annotation matrix from GRangesList
MatrixOrmatrix
: get annotation matrix from Matrix or matrix
data.frame
: get annotation matrix from data.frame
list
: get annotation matrix from list
character
: get annotations from bed files
Alicia Schep
# First get example counts data(mini_counts, package = "chromVAR") # Get annotations from genomic ranges list library(GenomicRanges) library(SummarizedExperiment) my_annotation_granges <- GRangesList(GRanges("chr1", ranges = IRanges(start = c(566763,805090), width = 8)), GRanges("chr1", ranges = IRanges(start = c(566792,895798), width = 8))) anno_ix <- getAnnotations(my_annotation_granges, rowRanges = rowRanges(mini_counts))