grFromElementString: Convert a genomic element string into an GRanges object.

In jefferys/FusionExpressionPlot: Plot Expression Profiles for Fused Genes

Description

Parses a genomic elements string into ranges, then adds a specified chromosome and strand and returns a GRanges object. The elements string parsed by default looks like:

    "1-100,3-500,2-3" 

Usage

grFromElementString(elementString, chr, strand = "*",
  betweenDelim = "\\s*,\\s*", fromDelim = "\\s*-\\s*")

Arguments

elementString	The string to parse into genomic ranges.
chr	The chromosome for the genomic ranges.
strand	The strand for the chromosome, must be '*', '+' or '-'. Defaults to '*' if not specified.
betweenDelim	The sequence delimiter, usually use the default '\s*,\s*'. Can be any regular expression.
fromDelim	The start-end position separator, usually use the default '\s*-\s*'. Can be any regular expression.

Details

Spaces around the between delimiter ',' and the from delimiter '-' are ignored; other delimiters (regular expressions) can be specified. All elements must be on the same sequence block (chromosome) and must be on the same strand (by default '*' for unspecified). Positions are given in 1 based coordinates as if on the positive strand with the low position first and the high position second. Actual positions would be reversed if on the negative strand.

Value

A GRanges object based on the input elements, with ranges sorted by start and then end position

jefferys/FusionExpressionPlot documentation built on May 19, 2019, 3:59 a.m.