Import-Matrix: Import data from matrix, cell and genes directly.

In bioinfoDZ/RISC: Robust Integration of Single-Cell RNA-Seq Datasets

Import data from matrix, cell and genes directly.

Description

Import data set from matrix, cell and genes directly, the customer needs three files: a matrix file including gene expression values: raw counts/UMIs (rows for genes while columns for cells), a cell file (whose row.name are equal to the col.name of the matrix), and a gene file whose row.name are the same as the row.name of the matrix. If row.names of the gene matrix are Ensembl ID, the customer need to transfer them to gene symbols manually.

Usage

readsc(count, cell, gene, is.filter = TRUE)

Arguments

count	Matrix with raw counts/UMIs.
cell	Data.frame with cell Barcode, whose row.name are equal to the col.name of the matrix.
gene	Data.frame with gene symbol, whose row.name are the same as the row.name of the matrix.
is.filter	Remove not expressed genes.

Value

RISC single cell dataset, including count, coldata, and rowdata.

Examples

mat0 = as.matrix(raw.mat[[1]])
coldata0 = as.data.frame(raw.mat[[2]])
coldata.obj = coldata0[coldata0$Batch0 == 'Batch3',]
matrix.obj = mat0[,rownames(coldata.obj)]
obj0 = readsc(count = matrix.obj, cell = coldata.obj, 
       gene = data.frame(Symbol = rownames(matrix.obj), 
       row.names = rownames(matrix.obj)), is.filter = FALSE)

bioinfoDZ/RISC documentation built on March 30, 2024, 9:19 p.m.