TEconstruct: Construct a taxaExp object.

In HangRuan1912/phyExp: the R package for analyzing expression evolution based on RNA-seq data

Description

constructor function for taxaExp objects This function takes in a read counts file and a gene information file. And construct a taxaExp object from which user can extract information for display or for further analysis.

Usage

TEconstruct(readCountsFP = NULL, geneInfoFP = NULL, taxa = "all",
  subtaxa = "all", normalize = c("TPM", "RPKM", "CPM"), rmOut = FALSE,
  verbose = FALSE)

Arguments

readCountsFP	a text file contains raw read counts data. Row names correspond with gene names, and column names correspond with taxon and subtaxon names.
geneInfoFP	a text file contains gene length information. Row names conrrespond with gene names, and column names correspond with taxon names.
taxa	one single string or a vector of strings specifying main taxa selected for constructing taxaExp object. Taxa names are extracted from row names given in gene length file. If one single string "all" is given, all the taxa in the row names will be matched and selected ("all" by default).
subtaxa	one single string or a vector of strings sepcifying sub taxa selected for constructing taxaExp object. If one single string "all" is given, all the sub taxa in the row names will be matched and selected ("all" by default).
normalize	a single string sepcifying normalization method ("TPM", "RPKM" or "CPM") while constructing taxaExp object ("TPM" by default).
rmOut	a logical sepcifying whether to remove read counts outliers while constructing taxaExp objects (TRUE by default).
verbose	a logical specifying whether to print more information on the screen while constructing taxaExp objects (FALSE by default).

Value

returns an object of class Taxa (S3 class, a list of taxonExp objects).

Examples

taxa.objects = TEconstruct(readCountsFP = system.file('extdata/tetraexp.read.counts.raw.txt', package = 'TreeExp'),
   geneInfoFP = system.file('extdata/tetraexp.length.ortholog.txt', package = 'TreeExp'),
   taxa = "all", subtaxa = c("Brain", "Cerebellum"), normalize = "TPM")

HangRuan1912/phyExp documentation built on July 15, 2019, 9:01 p.m.