tstatistics
computes either two-sample or paired t-statistics for a bunch of variables measured on the same objects, e.g. genewise t-statistics for a microarray experiment. PermNull
uses tstatistics
to generate a permutation distribution.
tstatistics(xdat, grp, logse = FALSE, paired = FALSE)
PermNull(xdat, grp, nperm = 100, seed = NULL, logse = FALSE, paired=FALSE)
xdat
, see Details.tstat
and optionally (if logse=TRUE
) a second column logse
. tstat
returns the same number of test statistics as rows in xdat
and in the same order, PermNull
does the same for consecutive permuations of the grouping variable grp
.If the argument seed
is specified, PermNull
adds an attribute of the same name to the returned data frame.
tstatistics
is a fairly fast replacement for function mt.teststat
in package multtest, which is written exlusively in R and does not require loading half the Bioconductor infrastructure packages before doing anything. As such, it is used for computing the default test statistics by fdr1d
and fdr2d
.Note that for the paired test, tstatistics
requires the same data structure as mt.teststat
: columns belonging to the same pair must be consecutive (though not necessarily in the same order throughout, as grp will indicate the order). The function checks for this and barfs if it does not hold.
PermNull
returns the t-statistics and optionally the logarithmized standard errors of the mean for a specified number of permutations.
Both functions are not especially economic in using memory, and collecting the whole set of permutations like PermNull
does instead of binning and counting them directly as they come is inherently wasteful.
fdr1d
, fdr2d
, examples in tMixture