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
)

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), TRUE: include softclips in size

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

Converted GRanges object

See Also

Other utils: bedToGR(), fimport(), findFa(), fread.bed(), optimizeReads(), readBam(), readWig()


[Package ORFik version 1.6.9 Index]