rowTtest-methods: Student's t-test for rows

In viper: Virtual Inference of Protein-activity by Enriched Regulon analysis

Description

This function performs a Student's t-test on each row of a matrix

Usage

rowTtest(x, ...)

## S4 method for signature 'matrix'
rowTtest(x, y = NULL, mu = 0,
  alternative = "two.sided")

## S4 method for signature 'ExpressionSet'
rowTtest(x, pheno, group1, group2 = NULL,
  mu = 0, alternative = "two.sided")

Arguments

x	ExpressionSet object or Numerical matrix containing the test samples
...	Additional parameters added to keep compatibility
y	Optional numerical matrix containing the reference samples. If ommited x will be tested against mean = mu
mu	Number indicating the alternative hypothesis when y is ommited
alternative	Character string indicating the tail for the test, either two.sided, greater or lower
pheno	Character string indicating the phenotype data to use
group1	Vector of character strings indicating the category from phenotype pheno to use as test group
group2	Vector of character strings indicating the category from phenotype pheno to use as control group

Value

List of Student-t-statistic (statistic) and p-values (p.value)

Examples

data(bcellViper, package="bcellViper")
d1 <- exprs(dset)
res <- rowTtest(d1[, 1:10], d1[, 11:20])
res$statistic[1:5, ]
res$p.value[1:5, ]
data(bcellViper, package="bcellViper")
res <- rowTtest(dset, "description", "CB", "N")
res$statistic[1:5, ]
res$p.value[1:5, ]

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

       ADA       CDH2       MED6      NR2E3      ACOT8 
0.56560137 0.62804829 0.77505513 0.07692461 2.64962490 
      ADA      CDH2      MED6     NR2E3     ACOT8 
0.5786478 0.5378599 0.4483700 0.9395321 0.0163018 
      ADA      CDH2      MED6     NR2E3     ACOT8 
7.7152636 1.2599771 0.3076719 0.1191403 2.5808352 
         ADA         CDH2         MED6        NR2E3        ACOT8 
5.663018e-05 2.431888e-01 7.661897e-01 9.081016e-01 3.257398e-02 

viper documentation built on Nov. 8, 2020, 7:37 p.m.