Read gene expression data from a file, sorted by a phylogenetic tree

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Description

This funciton will read in gene expression data from a text file and format it for downstream analysis. In particular, it will ensure that species are sorted appropriately given the phylogenetic tree and that the data is appropriately normalized by one species

Usage

1
read.exp(filename, phy, transpose = FALSE, normalize = 1, sep = "\t")

Arguments

filename

expression data file. Ideally, rows correspond to species and columns correspond to genes. First column should be species names, first row should be gene names. If the file is formatted in a transpose (i.e. genes are rows and species are columns) then see the transpose argument

phy

an ape-format phylogenetic tree containing all the species that have gene expressiond data. The tip labels of phy should correspond to the species names in the gene expression data file

transpose

a logical indicating whether to transpose the data from the input file. Only necessary if the input file has rows corresponding to genes and columns corresponding to species

normalize

indicates which species to normalize by. If normalization is undesired (unlikely) set to 0.

sep

the character that separates entries in the expression file

Value

A matrix containing gene expression data, in which rows correspond to species and columns correspond to genes

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