tileCount2 {NADfinder} | R Documentation |
Perform overlap queries between reads and genome by sliding windows Count reads over sliding windows.
tileCount2(reads, windowSize = 50000, restrict = paste0("chr", c(1:19, "X", "Y")), step = 1000, filter = 0, pe = "both")
reads |
An object that represents the names and path of the bam files to be counted. If reads are more than 1 bam files, it should be a vector of character with full path. This funciton now if for paired end reads |
windowSize |
numeric(1) or integer(1). Size of the windows. |
restrict |
restrict to a set of chromosomes, default to mouse chromosomes. |
step |
numeric(1) or integer(1). Step of generating silding windows. |
filter |
default to 0 without filtering |
pe |
a character string indicating whether paired-end data is present; set to "none", "both", "first" or "second" |
return a summarized experiment object with chromosome-level depth information for each input sample as metadata.
A RangedSummarizedExperiment object. The assays slot holds the counts, rowRanges holds the annotation from the sliding widows of genome. metadata contains lib.size.chrom for holding chromosome-level sequence depth
Jun Yu
if (interactive()) { fls <- list.files(system.file("extdata", package="NADfinder"), recursive=FALSE, pattern="*bam$", full=TRUE) names(fls) <- basename(fls) se <- tileCount2(reads = fls, windowSize=50000, step=10000) }