create the abundance matrix from a collection of the metagenomics

as.abundance_matrix {geneExpression}

R Documentation

create the abundance matrix from a collection of the metagenomics

Description

abundance data

Usage

as.abundance_matrix(samples,
    normalized = FALSE);

Arguments

samples

a tuple list of the abundance data: the slot key of the list is the sample id and the slot value is the abundance data of the corresponding sample, which can be a collection of the IExpressionValue object, a tuple list of the numeric value, or a dictionary object of the abundance data(the dictionary key is the taxonomy id and the value is the abundance value).

normalized

normalize the generated abundance matrix data? if this parameter is TRUE, then the abundance value of each sample column will be normalized as a relative abundance value. [as boolean]

env

the R# runtime environment object. [as Environment]

Details

a warning message will be pushed into the R# environment message buffer if the abundance data of some sample is nothing, and such kind of the sample will be skipped, an NotImplementedException will be thrown if the input data is not a tuple list object or the abundance data type is not supported.

Authors

phenotype_kit

Value

a Matrix abundance matrix object that the rows are the taxonomy features and the columns are the input samples.

clr value class

Matrix

[Package geneExpression version 1.0.0.0 Index]