lineup2ex {lineup2}

Example dataset for lineup2 package

Description

Example dataset for lineup2 package, with gene expression data for a selected set of 200 genes on two tissues on a set of about 500 mice, with 100 genes chosen to be highly correlated between the two tissues and 100 chosen at random.

Usage

data(lineup2ex)

Format

List of two matrices, with gene expression data for gastrocnemius muscle (gastroc) and pancreatic islets (islet), at a selected set of 200 genes (100 are highly correlated between the two tissues, and 100 others chosen at random). The matrices have samples as rows and genes as columns. The row names are sample identifiers. There are 498 samples for gastroc and 499 samples for islet, with 497 samples in common.

Source

https://phenome.jax.org/projects/Attie1

References

Broman KW, Keller MP, Broman AT, Kendziorski C, Yandell BS, Sen Ś, Attie AD (2015) Identification and correction of sample mix-ups in expression genetic data: A case study. G3 5:2177–2186

Tian J, Keller MP, Oler AT, Rabaglia ME, Schueler KL, Stapleton DS, Broman AT, Zhao W, Kendziorski C, Yandell BS, Hagenbuch B, Broman KW, Attie AD (2015) Identification of the bile acid transporter Slco1a6 as a candidate gene that broadly affects gene expression in mouse pancreatic islets. Genetics 201:1253–1262

Examples

data(lineup2ex)
common_ind <- align_matrix_rows(lineup2ex$gastroc, lineup2ex$islet)