alignData: align genome data at specified coordinates (e.g. TSS)

In raim/segmenTools: Tools for Functional Genome Exploration

align genome data at specified coordinates (e.g. TSS)

Description

align genome data at specified coordinates (e.g. TSS)

Usage

alignData(
  coors,
  data,
  dst = 500,
  chrS,
  coorCols = c(chr = "chr", position = "coor", strand = "strand"),
  reverse = c("-", -1)
)

Arguments

coors	genome positions (chromosome, coordinate, strand) at which data will be aligned (TODO: allow start/end coors and set NA if beyond)
data	genome data to be aligned; NOTE, that currently this is required to be fully expanded matrix covering each chromosome position, i.e. nrow(data)==max(chrS) (TODO: allow non-expanded data)
dst	upstream/downstream length to be aligned
chrS	the chromosome index, indicating the start position of each chromosome in data, derived from chromosome length information, see function getChrSum
coorCols	ordered string vector providing the column names of coordinate columns to be used; must be of length 3 and provide in order: chromosome number (refering to argument chrS), position and strand (see argument reverse)
reverse	a vector of possible reverse strand indicators, all other values in the strand column will be taken as forward strand!

raim/segmenTools documentation built on April 25, 2024, 10:14 a.m.