combine_Y_refs {dtangle}

Row-binds Y with references and generates pure_samples.

Description

Row-binds Y with references and generates pure_samples.

Usage

combine_Y_refs(Y, references, pure_samples)

Arguments

Y

Expression matrix.

(Required) Two-dimensional numeric. Must implement as.matrix.

Each row contains expression measurements for a particular sample. Each columm contains the measurements of the same gene over all individuals. Can either contain just the mixture samples to be deconvolved or both the mixture samples and the reference samples. See pure_samples and references for more details.

references

Cell-type reference expression matrix.

(Optional) Two-dimensional numeric. Must implement as.matrix. Must have same number of columns as Y. Columns must correspond to columns of Y.

Each row contains expression measurements for a reference profile of a particular cell type. Columns contain measurements of reference profiles of a gene. Optionally may merge this matrix with Y and use pure_samples to indicate which rows of Y are pure samples. If pure_samples is not specified references must be specified. In this case each row of references is assumed to be a distinct cell-type. If both pure_samples and references are specified then multiple rows of references may refer be the same cell type, and pure_samples specifies to which cell-type each row of references corresponds.

pure_samples

The pure sample indicies.

(Optional) List of one-dimensional integer. Must implement as.list.

The i-th element of the top-level list is a vector of indicies (rows of Y or references) that are pure samples of type i. If references is not specified then this argument identifies which rows of Y correspond to pure reference samples of which cell-types. If references is specified then this makes same idenficiation but for the references matrix instead.