comparison region_motif_intersect.r @ 37:76e108a19e64 draft

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36:b868314320e2

# Description: Takes a bed file of target regions and counts intersections
# of each motif (in separately installed tabix database) and target regions.
# Author: Jeremy Liu
# Email: [e-mail]
# Date: 15/02/11
# Note: This script is meant to be invoked with the following command
# R --slave --vanilla -f ./region_motif_intersect.r --args <db_bgz> <db_tbi> <inbed> <outtab>
# Dependencies: region_motif_data_manager

# Auxiliary function to concatenate multiple strings
concat <- function(...) {
  input_list <- list(...)
  return(paste(input_list, sep="", collapse=""))

startTime = Sys.time()
cat("Running ... Started at:", format(startTime, "%a %b %d %X %Y"), "...\n")

# Load dependencies
cat("Loading dependencies...\n")
suppressPackageStartupMessages(library(Rsamtools, quietly=TRUE))

# Initializing hash table (as env) with motif names and loading tabix file
cat("Loading motif database and initializing hash table...\n")
motifTable = new.env()
motifTbx <- TabixFile(motifDB_bgz)

37:76e108a19e64

# Description: Takes a bed file of target regions and counts intersections
# of each motif (in separately installed tabix database) and target regions.
# Author: Jeremy Liu
# Email: [e-mail]
# Date: 15/02/11
# Note: This script can be invoked with the following command
# R --slave --vanilla -f ./region_motif_intersect.r --args <db_bgz> <db_tbi> <inbed> <outtab>
# Dependencies: region_motif_data_manager, Rsamtools

# Auxiliary function to concatenate multiple strings
concat <- function(...) {
  input_list <- list(...)
  return(paste(input_list, sep="", collapse=""))

startTime = Sys.time()
cat("Running ... Started at:", format(startTime, "%a %b %d %X %Y"), "...\n")

# Load dependencies
cat("Loading dependencies...\n")
suppressPackageStartupMessages(library(Rsamtools, quietly=TRUE)) # NEED TO HANDLE INSTALLATION

# Initializing hash table (as env) with motif names and loading tabix file
cat("Loading motif database and initializing hash table...\n")
motifTable = new.env()
motifTbx <- TabixFile(motifDB_bgz)