computeSlidingT {Ringo} | R Documentation |
Function to compute sliding (regularized) one- or two-sample T statistics on a tiling expression set.
computeSlidingT(xSet, probeAnno, allChr = c(1:19, "X", "Y"), test = "one.sample", grouping = NULL, winHalfSize = 400, min.probes = 5, checkUnique = TRUE, uniqueCodes = c(0), verbose = TRUE)
xSet |
Object of class ExpressionSet holding the
normalized probe intensity data |
probeAnno |
Environment holding the genomic positions of probes in the ExpressionSet |
allChr |
Character vector of all chromosomes in genome |
test |
character; one of one.sample or two.sample |
grouping |
factor vector of length equal to number of samples, currently not required |
winHalfSize |
Half the size of the window centered at a probe position, in which all other probes contribute to the calculation of the mean and standard deviation. |
min.probes |
integer; if less probes are in the sliding window, NA instead of the mean and sd is returned. This is meant to avoid to computing non-meaningful means and standard deviations. If unwanted, set this to 1 or less |
checkUnique |
logical; indicates whether the uniqueness indicator of probe matches from the probeAnno environment should be used. |
uniqueCodes |
numeric; which numeric codes in the chromosome-wise match-uniqueness elements of the probeAnno environment indicate uniqueness? |
verbose |
logical; detailed progress output to STDOUT? |
An object of class ExpressionSet
, holding the T statistics
values for the probes of the supplied ExpressionSet. The number of
results samples is the number of levels in the supplied factor
grouping
.
the option two.sample
is not implemented yet
Joern Toedling toedling@ebi.ac.uk
exDir <- system.file("exData",package="Ringo") load(file.path(exDir,"exampleProbeAnno.rda")) load(file.path(exDir,"exampleX.rda")) tX <- computeSlidingT(exampleX, probeAnno=exProbeAnno, allChr=c("9"), winHalfSize=400) sampleNames(tX) <- "t-Stat_Suz12vsTotal" if (interactive()){ par(mfrow=c(1,1)) chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000), ylim=c(-2,8.5), probeAnno=exProbeAnno, gff=exGFF) chipAlongChrom(tX, chrom="9", xlim=c(34318000,34321000), probeAnno=exProbeAnno, itype="l", ilwd=4, paletteName="Spectral", add=TRUE) }