convertToOneBasedRanges {ORFik}R Documentation

Convert a GRanges Object to 1 width reads

Description

There are 4 ways of doing this 1. Take 5' ends, reduce away rest (5prime) 2. Take 3' ends, reduce away rest (3prime) 3. Tile and include all (tileAll) 4. Take middle point per GRanges (middle)

Usage

convertToOneBasedRanges(gr, method = "5prime", addScoreColumn = FALSE,
  addSizeColumn = FALSE)

Arguments

gr

GRanges, GAlignment Object to reduce

method

the method to reduce, see info. (5prime defualt)

addScoreColumn

logical (FALSE), if TRUE, add a score column that sums up the hits per position.

addSizeColumn

logical (FALSE), if TRUE, add a size column that for each read, that gives original width of read.

Details

Many other ways to do this have their own functions, like startCodons and stopCodons.

Value

Converted GRanges object

See Also

Other utils: bedToGR, findFa, fread.bed, is.gr_or_grl, is.grl, validGRL


[Package ORFik version 1.4.0 Index]