Description Usage Arguments Value Examples
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.
1 2 3 |
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 |
subtaxa |
one single string or a vector of strings sepcifying sub taxa selected for
constructing |
normalize |
a single string sepcifying normalization method ("TPM", "RPKM" or "CPM")
while constructing |
rmOut |
a logical sepcifying whether to remove read counts outliers
while constructing |
verbose |
a logical specifying whether to print more information on the screen
while constructing |
returns an object of class Taxa
(S3 class, a list of taxonExp
objects).
1 2 3 4 | taxa.objects = tExpConstruct(
readCountsFP = system.file('extdata/tetraexp.read.counts.raw.txt', package = 'AnceTran'),
geneInfoFP = system.file('extdata/tetraexp.length.ortholog.txt', package = 'AnceTran'),
taxa = "all", subtaxa = c("Brain", "Cerebellum"), normalize = "TPM")
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