R/data.R

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)

#===============================================================================
# data.R
#===============================================================================

#' @title SNVs associated with allele-specific binding (ASB)
#'
#' @details
#' \code{
#'   ===========
#'   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.
#' }
#' @format A data frame with 8806 rows and 12 variables
#' @source \url{http://alleledb.gersteinlab.org/download/}
"asb"

#' @title SNVs that are accessible to allele-specific binding
#'
#' @details
#' \code{
#'   ===========
#'   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.
#' }
#' @format A data frame with 276589 rows and 12 variables
#' @source \url{http://alleledb.gersteinlab.org/download/}
"accb"