mouse_to_human_homologs: Table of Human->Mouse orthologs for all human genes

In EWCE: Expression Weighted Celltype Enrichment

Description

A dataset containing the MGI and HGNC symbols, Human and Mouse Entrez and Ensembl gene IDs for all human orthologs for mouse genes. Whenin the mouse genes are defined based on a list of all MGI markers from the MGI website (downloaded as MRK_List2.rpt file from http://goo.gl/mjf2GQ)

Usage

mouse_to_human_homologs

Format

An object of class data.frame with 21508 rows and 6 columns.

Examples

## Not run: 
## The code to prepare the .Rda file file from the marker file is:
markers = read.csv("MRK_List2.rpt",sep="\t")
genes = markers[markers$Feature.Type=="protein coding gene",]
listMarts(host="www.ensembl.org")
human <- useMart(host="www.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
mouse <- useMart(host="www.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl")
mouse_to_human_homologs = getLDS(attributes = c("mgi_symbol","entrezgene","ensembl_gene_id"),
                                 filters = "mgi_symbol", values = genes$Marker.Symbol,
                                 mart = mouse,
                                 attributesL = c("hgnc_symbol","ensembl_gene_id","entrezgene"), martL = human)
save(mouse_to_human_homologs,file="mouse_to_human_homologs.Rda")

## End(Not run)

EWCE documentation built on May 31, 2017, 3:16 p.m.