make.gene.summary: Make an Entrez Gene Summary table which includes the genes...

In drmjc/genomics: Genomics related functions.

Description

Data is retreived from "gene2refseq" and "gene_info" available from: "ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz" and "ftp.ncbi.nih.gov/gene/DATA/gene_info.gz" Algorithm: The best genomic location is determined from gene2refseq file (see import.gene2refseq) The relevant columns from gene_info are kept (see import.gene_info)

Usage

  make.gene.summary(outfile = "/biomirror/mouse/Gene/gene.summary.mm.txt",
    taxid = 10090)

Arguments

outfile	undocumented parameter
taxid	undocumented parameter

Value

a data.frame with the following columns: c("GeneID", "Symbol", "Description", "Synonym", "GenbankID", "mgiID", "Chr", "Start", "Stop", "Strand", "cM") GeneID Symbol Description 1 11287 Pzp pregnancy zone protein 2 11298 Aanat arylalkylamine N-acetyltransferase 3 11302 Aatk apoptosis-associated tyrosine kinase 4 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1 5 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4 6 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2 Synonyms GenbankID mgiID 1 A1m /// A2m /// AI893533 /// MAM NM_007376 MGI:87854 2 MGC151344 /// Nat-2 /// Nat4 /// SNAT NM_009591 MGI:1328365 3 AATYK /// mKIAA0641 NM_007377 MGI:1197518 4 Abc1 NM_013454 MGI:99607 5 AW050280 /// Abc10 /// Abcr /// D430003I15Rik /// RmP NM_007378 MGI:109424 6 AI413825 /// Abc2 /// D2H0S1474E /// mKIAA1062 NM_007379 MGI:99606 Chr Start Stop Strand cM 1 6 1.28e+08 1.28e+08 - 62.0 2 11 1.16e+08 1.16e+08 + 70.0 3 11 1.20e+08 1.20e+08 - NA 4 4 5.31e+07 5.32e+07 - 23.1 5 3 1.22e+08 1.22e+08 + 61.8 6 2 2.53e+07 2.53e+07 + 12.6 checked with Mouse, Rat and Humans.

Author(s)

Mark Cowley, 19/3/07

drmjc/genomics documentation built on May 15, 2019, 2:22 p.m.