determineTSR {TSRchitect} | R Documentation |
determineTSR
Identifies TSRs from
entire TSS datasets as specified.
determineTSR( experimentName, n.cores, tssSetType, tssSet, tagCountThreshold, clustDist, ... ) ## S4 method for signature ## 'tssObject,numeric,character,character,numeric,numeric' determineTSR( experimentName, n.cores = 1, tssSetType = c("replicates", "merged"), tssSet = "all", tagCountThreshold = 1, clustDist = 20, writeTable = FALSE, mixedorder = FALSE )
experimentName |
an object of class tssObject containing information in slot @tssTagData |
n.cores |
the number of cores to be used for this job. ncores=1 means serial execution of function calls (numeric) |
tssSetType |
specifies the set to be clustered. Options are "replicates" or "merged". (character) |
tssSet |
default is "all"; if a single TSS dataset is desired, specify tssSet number (character) |
tagCountThreshold |
the number of TSSs required at a given position for it to be considered in TSR identification. (numeric) |
clustDist |
the maximum distance of TSSs between two TSRs in base pairs. (numeric) |
writeTable |
specifies whether the output should be written to a table. (logical) |
mixedorder |
a logical specifying whether the sequence names should be ordered alphanumerically in the output table ("10" following "9" rather than "1"). (logical) |
creates a list of GenomicRanges-containing TSR positions in slot @tsrData of the returned tssObject object
An example similar to this one can be found in the vignette (/inst/doc/TSRchitect.Rmd)
load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect")) tssObjectExample <- determineTSR(experimentName=tssObjectExample, n.cores=1, tssSetType="replicates", tssSet="1", tagCountThreshold=25, clustDist=20, writeTable=FALSE)