findPeaks {DEScan2} | R Documentation |
This function calls peaks from bed or bam inputs using a variable window scan with a poisson model using the surrounding maxCompWinWidth (10kb) as background.
findPeaks(files, filetype = c("bam", "bed"), genomeName = NULL, binSize = 50, minWin = 50, maxWin = 1000, zthresh = 10, minCount = 0.1, minCompWinWidth = 5000, maxCompWinWidth = 10000, outputFolder = "Peaks", save = TRUE, force = TRUE, verbose = FALSE, sigwin = 10, onlyStdChrs = TRUE, chr = NULL, BPPARAM = BiocParallel::bpparam())
files |
Character vector containing paths of files to be analyzed. |
filetype |
Character, either "bam" or "bed" indicating format of input file. |
genomeName |
the code of the genome to use as reference for the input files. (cfr. constructBedRanges function parameters) |
binSize |
Integer size in bases of the minimum window for scanning, 50 is the default. |
minWin |
Integer indicating the minimum window size in bases notation. |
maxWin |
Integer indicating the maximum window size in bases notation. |
zthresh |
Cuttoff value for z-scores. Only windows with greater z-scores will be kept, default is 10. |
minCount |
A small constant (usually no larger than one) to be added to the counts prior to the log transformation to avoid problems with log(0). |
minCompWinWidth |
minimum bases width of a comparing window for Z-score. |
maxCompWinWidth |
maximum bases width of a comparing window for Z-score. |
outputFolder |
A string, Name of the folder to save the Peaks (optional) if the directory doesn't exist, it will be created. (Default is "Peaks") |
save |
Boolean, if TRUE files will be saved in a "./Peaks/chr*" directory created (if not already present) in the current working directory. |
force |
a boolean flag indicating if to force output overwriting. |
verbose |
if to show additional messages |
sigwin |
an integer value used to compute the length of the signal of a peak (default value is 10). |
onlyStdChrs |
a flag to work only with standard chromosomes. (cfr. constructBedRanges function parameters). |
chr |
if not NULL, a character like "chr#" indicating the chromosomes to use. |
BPPARAM |
object of class |
A GRangesList where each element is a sample. Each GRanges represents the founded peaks and attached the z-score of the peak as mcols.
bam.files <- list.files(system.file("extdata/bam", package = "DEScan2"), full.names = TRUE) peaks <- findPeaks(files=bam.files[1], filetype="bam", genomeName="mm9", binSize=50, minWin=50, maxWin=1000, zthresh=5, minCount=0.1, sigwin=10, minCompWinWidth=5000, maxCompWinWidth=10000, save=FALSE, onlyStdChrs=TRUE, chr=NULL, verbose=FALSE) head(peaks)