convertToOneBasedRanges: Convert a GRanges Object to 1 width reads
In JokingHero/ORFik: Open Reading Frames in Genomics

convertToOneBasedRanges

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)
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.

Usage

convertToOneBasedRanges(
  gr,
  method = "5prime",
  addScoreColumn = FALSE,
  addSizeColumn = FALSE,
  after.softclips = TRUE,
  along.reference = FALSE,
  reuse.score.column = TRUE
)

Arguments

`gr`	GRanges, GAlignment or GAlignmentPairs object to reduce.
`method`	character, default `"5prime"`, the method to reduce ranges, see NOTE for more info.
`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 collapsed hits. A useful compression. If addSizeColumn is FALSE, it will not differentiate between reads with same start and stop, but different length. If addSizeColumn is FALSE, it will remove it. Collapses after conversion.
`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. If collapsing reads, each unique range will be grouped also by size.
`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.
`reuse.score.column`	logical (TRUE), if addScoreColumn is TRUE, and a score column exists, will sum up the scores to create a new score. If FALSE, will skip old score column and create new according to number of replicated reads after conversion. If addScoreColumn is FALSE, this argument is ignored.

Details

NOTE: Note: For cigar based ranges (GAlignments), the 5' end is the first non clipped base (neither soft clipped or hard clipped from 5'). This is following the default of bioconductor. For special case of GAlignmentPairs, 5prime will only use left (first) 5' end and read and 3prime will use only right (last) 3' end of read in pair. tileAll and middle can possibly find poinst that are not in the reads since: lets say pair is 1-5 and 10-15, middle is 7, which is not in the read.

Value

Converted GRanges object

Examples

gr <- GRanges("chr1", 1:10,"+")
# 5 prime ends
convertToOneBasedRanges(gr)
# is equal to convertToOneBasedRanges(gr, method = "5prime")
# 3 prime ends
convertToOneBasedRanges(gr, method = "3prime")
# With lengths
convertToOneBasedRanges(gr, addSizeColumn = TRUE)
# With score (# of replicates)
gr <- rep(gr, 2)
convertToOneBasedRanges(gr, addSizeColumn = TRUE, addScoreColumn = TRUE)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.