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


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


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



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


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


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


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


the character that separates entries in the expression file


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

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