make.stat: Calculates several statistices on read counts

In pmoulos/metaseqr: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

Description

Returns a matrix of statistics calculated for a set of given samples. Internal use.

Usage

    make.stat(samples, data.list, stat, export.scale)

Arguments

samples	a set of samples from the dataset under processing. They should match sample names from sample.list. See also the main help page of metaseqr.
data.list	a list containing natural or transformed data, typically an output from make.transformation.
stat	the statistics to calculate. Can be one or more of "mean", "median", "sd", "mad", "cv", "rcv". See also the main help page of metaseqr.
export.scale	the output transformations used as input also to make.transformation.

Value

A matrix of statistics calculated based on the input sample names. The different data transformnations are appended columnwise.

Author(s)

Panagiotis Moulos

Examples

data.matrix <- round(1000*matrix(runif(400),100,4))
rownames(data.matrix) <- paste("gene_",1:100,sep="")
colnames(data.matrix) <- c("C1","C2","T1","T2")
tr <- make.transformation(data.matrix,c("log2","vst"))
st <- make.stat(c("C1","C2"),tr,c("mean","sd"),c("log2","vst"))

pmoulos/metaseqr documentation built on Dec. 29, 2020, 5:56 a.m.