melanoma_data: Example dataset containing data from lymph nodes from...
In GfellerLab/EPIC: Estimate the Proportion of Immune and Cancer cells

melanoma_data

R Documentation

Example dataset containing data from lymph nodes from patients with metastatic melanoma.

Description

This is the dataset measured in Racle et al., 2017, eLife. It contains the gene expression from lymph node samples from four patients with melanoma, and it contains also the proportions of the main immune cell types and of melanoma cells, as measured by FACS.

Usage

melanoma_data

Format

This is a list of 3 elements:

$counts: (matrix of 49902 genes x 4 donors) The TPM normalized counts from the four donors. It has been obtained by mapping RNA-seq data to hg19 genome with help of RSEM. Ensembl ID were then converted to gene names, and genes with duplicated entries were merged together by summing their counts.
$cellFractions.obs: (matrix of 4 donors x 6 cell types) The proportions of the different cell types measured by FACS (the "other_cells" correspond to the live cells without any marker of the other given cell types).
$cellFractions.pred: (matrix of 4 donors x 8 cell types) The proportions of the different cell types, as predicted by EPIC based on the reference profiles TRef.