PBMC_example: PBMC_scMappR

In DustinSokolowski/scMappR: Single Cell Mapper

Description

Data for scMappR_and_pathway_analysis example.

Usage

data(PBMC_example)

Format

A list containing three data frames, normalized count data, a signature matrix, and a list of differentially expressed genes.

bulk_normalized

A 3231 x 9 matrix where rows are genes, columns are samples, and the matrix is filled with CPM normalized counts.

odds_ratio_in

A 2336 x 7 matrix where rows are genes, columns are cell-types and matrix is filled with the odds-ratio that a gene is in each cell-type.

bulk_DE_cors

A 59 x 3 matrix of sex-specific genes found between male and female PBMC samples (female biased = upregulated). row and rownames are genes, columns are gene name, FDR adjusted p-value, and log2 fold-change. DEGs were computed with DESeq2 and genes with a log2FC > 1 were kept.

Details

A named list called "PBMC_example" containing the count data, signature matrix, and DEGs. The count data and signature matrix are shortened to fit the size of the package and do not reflect the paper.

Examples

data(PBMC_example)

DustinSokolowski/scMappR documentation built on July 7, 2020, 5:44 p.m.