annotateLoops.dge {diffloop} | R Documentation |
annotateLoops.dge
adds columns to the rowData slot of a loops
object that shows summary statistics corresponding TSS of a gene name
based on the genes.tss rowData column. This function should be used
following the keepEPloops
function.
annotateLoops.dge(lto, deseq_res, multiple = FALSE) ## S4 method for signature 'ANY' annotateLoops.dge(lto, deseq_res, multiple = FALSE)
lto |
A loops object whose loops will be annotated |
deseq_res |
A data.frame |
multiple |
Annotate loops with multiple TSS? Default = FALSE |
This function links enhancer-promoter loops and differential gene expression results. The rownames of the deseq_res slots should correspond to the gene names in the gene.tss column of the rowData slot of the loops object. The function returns a loops object if multiple is specified as FALSE which is the case by default. Otherwise, if multiple is TRUE, then this function returns a data frame since each loop may have more than moe TSS. One can reproduce this dataframe quickly when multiple = FALSE using the summary() function on the returned loops object.
A loops object if multiple = FALSE or data frame if multiple = TRUE
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/') load(rda) h3k27ac_j <- system.file('extdata','Jurkat_H3K27ac_chr1.narrowPeak',package='diffloop') h3k27ac <- rmchr(padGRanges(bedToGRanges(h3k27ac_j), pad = 1000)) promoter <- padGRanges(getHumanTSS(c('1')), pad = 1000) #small.ep <- keepEPloops(loops.small, h3k27ac, promoter) #ADD SOMETHING HERE.