make.stat: Calculates several statistices on read counts

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

1
    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

1
2
3
4
5
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-local documentation built on May 9, 2019, 1:13 a.m.