Description Usage Arguments Details Value Examples
CTGSA
CTGSA : Covariance Thresholding for Gene Set Analysis of Genetic Pathway Data
1 2 3 |
x |
an input matrix of dimension nobs x nvars. |
y |
a response variable where y=1 is the case and y=0 is control. |
out.type |
character of output type of statistic('stat') and p-value('pvalue'). |
percentile.type |
three threshold calculating types are supported as 'case-control', 'all', and 'user-defined'. To choose the threshold, 'case-control' computes the percentile with the first singular value for case and control. Percentile.type 'all' calculates the percentile with whole samples. The percentile is given by user in 'user-defined', and the threshold is then calculated for case and control. The default is case-control. |
percentile.user |
a numeric value of percentile in [0, 1]. To specify the percentile, give the percentile.type 'user-defined', and the integer value taken here will be used. |
nperm |
number of permuation - default is 1000. |
See the reference below for more information.
A list of a statistic, an optional pvalue and permuted statistics, and arguments used.
1 2 3 4 5 6 7 8 9 10 | x <- replicate(5, rnorm(100, 0, 1))
y <- rep(0:1, each=50)
CTGSA( x = x, y = y, out.type="stat", percentile.type = "all")
require(mnormt)
x <- rbind(rmnorm(50, rep(0, 5), diag(5) ),
rmnorm(50, rep(0, 5), outer(1:5, 1:5, function(i, j) 0.6^abs(i-j) ) ))
y <- rep(0:1, each=50)
CTGSA(x=x, y=y, out.type="pvalue", percentile.type = "case-control", nperm=1000)
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