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

Description Usage Arguments

View source: R/coor2index.R

Description

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

Usage

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

Arguments

coors

genome positions (position, chromosome, strand) at which data will be aligned

data

genome data to be aligned; NOTE, that currently this is required to be fully expanded matrix covering each position (TODO: allow non-expanded data)

dst

upstream/downstream length to be aligned (TODO: allow different upstream and downstream ranges) (TODO: allow individual ranges)

chrS

the chromosome index, indicating the start position of each chromosome in the continuous index, 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 Nov. 9, 2018, 5:38 p.m.