R: Convert a GRanges Object to 1 width reads

convertToOneBasedRanges {ORFik}

R Documentation

Convert a GRanges Object to 1 width reads

Description

There are 5 ways of doing this 1. Take 5' ends, reduce away rest (5prime) 2. Take 3' ends, reduce away rest (3prime) 3. Tile to 1-mers and include all (tileAll) 4. Take middle point per GRanges (middle) 5. Get original with metacolumns (None)

Usage

convertToOneBasedRanges(
  gr,
  method = "5prime",
  addScoreColumn = FALSE,
  addSizeColumn = FALSE,
  after.softclips = TRUE,
  along.reference = 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 unique range This will make each read unique, so that each read is 1 time, and score column gives the number of hits. A useful compression. If addSizeColumn is FALSE, it will not differentiate between reads with same start and stop, but different length.
`addSizeColumn`	logical (FALSE), if TRUE, add a size column that for each read, that gives original width of read. Useful if you need original read lengths. This takes care of soft clips etc.
`after.softclips`	logical (TRUE), include softclips in width. Does not apply if along.reference is TRUE.
`along.reference`	logical (FALSE), example: The cigar "26MI2" is by default width 28, but if along.reference is TRUE, it will be 26. The length of the read along the reference. Also "1D20M" will be 21 if by along.reference is TRUE. Intronic regions (cigar: N) will be removed. So: "1M200N19M" is 20, not 220.

Details

You can also do multiple at a time, then output is GRangesList, where each list group is the operation (5prime is [1], 3prime is [2] etc)

Many other ways to do this have their own functions, like startSites and stopSites etc. To retain information on original width, set addSizeColumn to TRUE. To compress data, 1 GRanges object per unique read, set addScoreColumn to TRUE. This will give you a score column with how many duplicated reads there were in the specified region.

NOTE: Does not support paired end reads for the moment!

Value