screen.cgh.mrna
).
Pairs samples in two data sets.
pint.data(data, info, impute = TRUE, replace.inf = TRUE, remove.duplicates)
pint.match(X, Y, max.dist = 1e7, chrs = NULL, useSegmentedData =
FALSE, impute = TRUE, replace.inf = TRUE, remove.duplicates = TRUE)
loc
or
bp
, which is middle location of probe, or as start
and
end
. Chromosome arm is given as arm
and chromosome as
chr
.
FALSE
, rows with
identical data are removed (option for pint.match)TRUE
, rows with identical
data are removed (in pint.data), or
duplicate signals from many-to-one matches are removed (in pint.match)TRUE
, missing values are imputed by
replacing them with random samples from a Gaussian
distribution following the mean and standard deviation
of the non-missing data points from the same sample.TRUE
, replace infinite values
with highest non-infinite values seen in the
data. Otherwise the calculation will halt.pint.data
returns a list with a matrix with sample data and a
data frame with chr
(chromosome), arm
(chromosome arm) and
loc
(location).pint.match
return a list with two data sets. These can be used in
screen.cgh.mrna
function.pint.match
goes through every sample in X
and
finds the nearest sample in Y
which is in the same chromosome
arm. If more than one sample in X
has same nearest sample in
Y
, all but one is discarded. Samples with longer distance
than max.dist
are discarded.
screen.cgh.mrna
,
screen.cgh.mir
,
fit.cgh.mir.byname
data(chromosome17)
newData <- pint.match(geneExp,geneCopyNum,max.dist=1000)
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