| 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)
}