TEconstruct: Construct a taxaExp object.

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

Description

Constructor function for taxaExp objects. This function takes in a expression value file from RNA-seq, and construct a taxaExp object from which user can extract information for display or for further analysis.

Usage

TEconstruct(ExpValueFP = NULL, taxa = "all", subtaxa = "all",
  rmOut = FALSE, verbose = FALSE)

Arguments

ExpValueFP	a text file contains processed expression data (RPKM or TPM for example). Row names correspond with gene names, and column names correspond with taxon and subtaxon 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).
rmOut	a logical sepcifying whether to remove expression 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(ExpValueFP = system.file('extdata/primate_brain_expvalues.txt',
 package = 'TreeExp'), taxa = "all", subtaxa = c("HIP", "CB"))

jingwyang/TreeExp documentation built on June 11, 2019, 6:17 p.m.