samr.internal: Internal samr functions

In samr: SAM: Significance Analysis of Microarrays

Description

Internal samr functions

Usage

ttest.func(x, y, s0 = 0, sd=NULL)
wilcoxon.func(x, y, s0 = 0)
onesample.ttest.func(x, y, s0 = 0, sd=NULL)
paired.ttest.func(x, y, s0 = 0, sd=NULL)
cox.func(x, y, censoring.status, s0 = 0)
multiclass.func(x, y, s0 = 0)
quantitative.func(x, y, s0 = 0)
patterndiscovery.func(x,s0=0, eigengene.number=1)
timearea.func(x, y, s0 = 0)
sumlengths(aa)
detec.slab(samr.obj, del, min.foldchange)
detec.horiz(samr.obj, cutlow, cutup, min.foldchange)
localfdr(samr.obj, min.foldchange, perc = 0.01, df = 10)
predictlocalfdr(smooth.object, d)
qvalue.func(samr.obj, sig, delta.table)
foldchange.twoclass(x, y, logged2)
foldchange.paired(x, y, logged2)
est.s0(tt, sd, s0.perc = seq(0, 1, by = 0.05))
permute(elem)
sample.perms(elem, nperms)
permute.rows(x)
insert.value(vec, newval, pos)
integer.base.b(x, b = 2)
varr(x, meanx = NULL)
mysvd(x, n.components=NULL)
getperms(y, nperms)
compute.block.perms(y, blocky, nperms)
parse.block.labels.for.2classes(y)
parse.time.labels.and.summarize.data(x, y, resp.type,time.summary.type)

check.format(y, resp.type, censoring.status = NULL)
samr.const.quantitative.response
samr.const.twoclass.unpaired.response
samr.const.survival.response
samr.const.multiclass.response
samr.const.oneclass.response
samr.const.twoclass.paired.response
samr.const.twoclass.unpaired.timecourse.response
samr.const.twoclass.paired.timecourse.response
samr.const.oneclass.timecourse.response
samr.const.patterndiscovery.response
resample(x, d, nresamp=20)
wilcoxon.unpaired.seq.func(xresamp, y)
wilcoxon.paired.seq.func(xresamp, y)
multiclass.seq.func(xresamp, y)
quantitative.seq.func(xresamp, y)
cox.seq.func(xresamp, y, censoring.status)
rankcol(x)
samr.compute.delta.table.seq(samr.obj, min.foldchange=0, dels=NULL)
samr.seq.null.err(samr.obj, min.foldchange, cutup, cutlow)
samr.seq.detec.slabs(samr.obj, dels, min.foldchange)
generate.dels(samr.obj, min.foldchange=0)
foldchange.seq.twoclass.paired(x, y, depth)
foldchange.seq.twoclass.unpaired(x, y, depth)
samr.compute.delta.table.array(samr.obj, min.foldchange=0, dels=NULL, nvals=50)
## S3 method for class 'SAMoutput'
plot(x, ...)
## S3 method for class 'SAMoutput'
print(x, ...)

Details

These are not to be called by the user.

Author(s)

Jun Li and Balasubrimanian Narasimhan and Robert Tibshirani

samr documentation built on May 1, 2019, 7:49 p.m.