LTLA
/ parallel_crossprod.R
Last active
September 22, 2018 17:01
Parallelized calculation of the cross-product, computed with as much memory efficiency as possible.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(BiocParallel) | |
| library(DelayedArray) | |
| #' @importFrom stats start end | |
| .grid_iterate <- function(x, grid = NULL) { | |
| b <- 0L | |
| function() { | |
| if (b == length(grid)) { | |
| return(NULL) | |
| } |
LTLA
/ intron_exon_counter.R
Last active
November 17, 2022 17:49
A script to count reads in introns and exons
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Reading in the annotation. | |
| library(TxDb.Mmusculus.UCSC.mm10.ensGene) | |
| intronic <- intronicParts(TxDb.Mmusculus.UCSC.mm10.ensGene, linked.to.single.gene.only=TRUE) | |
| exonic <- exonicParts(TxDb.Mmusculus.UCSC.mm10.ensGene, linked.to.single.gene.only=TRUE) | |
| IX <- data.frame(GeneID=intronic$gene_id, Chr=as.character(seqnames(intronic)), | |
| Start=start(intronic), End=end(intronic), Strand=strand(intronic), stringsAsFactors=FALSE) | |
| EX <- data.frame(GeneID=exonic$gene_id, Chr=as.character(seqnames(exonic)), | |
| Start=start(exonic), End=end(exonic), Strand=strand(exonic), stringsAsFactors=FALSE) |
NewerOlder