multi_tissue: data objects for multi-tissues mixing samples

In DeconRNASeq: Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data

Description

a list containing:

1) x.data:a data frame providing the RPKM of nine mixing samples.

2) x.signatures: a data frame providing the expression values from pure brain, muscle, lung, liver and heart samples.

3) x.signatures.filtered: a data frame providing the expression values from pure brain, muscle, lung, liver and heart samples after filtering.

4) x.signatures.filtered.optimal: a data frame providing the expression values from pure brain, muscle, lung, liver and heart samples used for the example in DeconRNA-Seq.

5)fraction: a data frame providing the fractions from 5 tissues in the mixing samples

Usage

multi_tissue

Format

A list 1) a matrix with all the genes' expression in the mixing samples: the first two columns are corresponding to the RefSeq accession numbers and gene symbols

2) a martix whose rows are gene symbols and columns are RPKM expressions from pure tissues.

3) a martix whose rows are gene symbols and columns are RPKM expressions from pure tissues: the genes with RPKM less than 200 within any of the five tissues have been filtered.

4) a martix whose rows are gene symbols and columns are RPKM expressions from pure tissues: based on the filtered signature matrix, the optimal number of genes have been selected for the deconvolution according to the condition numbers

5) a martix whose rows are mixing samples' name and columns are fractions from pure tissues including brain, muscle, lung, liver and heart

Author(s)

Ting Gong [e-mail] Joseph D. Szustakowski [e-mail]

Examples

data(multi_tissue)

DeconRNASeq documentation built on Nov. 8, 2020, 7:51 p.m.