accb: SNVs that are accessible to allele-specific binding

In anthony-aylward/chenimbalance: Allelic imbalance mapping procedure from Chen et al. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals (2016)

Description

SNVs that are accessible to allele-specific binding

Usage

accb

Format

A data frame with 276589 rows and 12 variables

Details

=========== CHANGELOG =========== v2.1 --same results from v2.0, with additional columns for alternate alleles and p values from the betabinomial test v2.0 --results produced from updated scripts (available under 'Scripts' section, v2.0, http://alleledb.gersteinlab.org/docs/) --minor debugs in scripts v1.0 --results in publication --------------------------------------------------- The columns are defined as follows: 1:chr : chromosome 2:start : SNV start position (0-based) 3:end : SNV end position (1-based) 4:TF_indiv_ASB : (in ASB) transcription factor ; individual ID (as in the 1000 Genomes Project) ; ASB TF_indiv_accB : transcription factor ; individual ID (as in the 1000 Genomes Project) ; accessible SNVs related to non-ASB gene_indiv_ASE : (in ASE) HGNC gene symbol or NA if not in any gene ; individual ID ; ASE gene_indiv_accE: HGNC gene symbol or NA if not in any gene ; individual ID ; accessible SNVs related to non-ASE 5:ref_allele : reference allele 6:alt_allele : alternate allele (multiple alleles are separated by ';') 7:cA : read counts for A 8:cC : read counts for C 9:cG : read counts for G 10:cT : read counts for T 11:p.betabinom : p values calculated from the betabinomial test in AlleleDB pipeline ** gene regions are defined in GENCODE v17.

Source

http://alleledb.gersteinlab.org/download/

anthony-aylward/chenimbalance documentation built on May 17, 2019, 12:50 p.m.