shiftFootprintsByExperiment {ORFik} | R Documentation

## Shift footprints of each file in experiment

### Description

Saves files to a specified location as .bed, it will include a score column containing read width.

### Usage

    shiftFootprintsByExperiment(
      df,
      out.dir = pasteDir(dirname(df$filepath[1]), "/pshifted/"),
      start = TRUE,
      stop = FALSE,
      top_tx = 10L,
      minFiveUTR = 30L,
      minCDS = 150L,
      minThreeUTR = 30L,
      firstN = 150L
    )

### Arguments

`df` | an ORFik `experiment`
`out.dir` | output directory for files, default: dirname(df$filepath[1]), making a /pshifted folder at that location
`start` | (logical) Whether to include predictions based on the start codons. Default TRUE.
`stop` | (logical) Whether to include predictions based on the stop codons. Default FASLE. Only use if there exists 3' UTRs for the annotation.
`top_tx` | (integer) Specify which transcripts to use for estimation of the shifts. By default we take top 10 top covered transcripts as they represent less noisy dataset. This is only applicable when there are more than 1000 transcripts.
`minFiveUTR` | (integer) minimum bp for 5' UTR during filtering for the transcripts. Set to NULL if no 5' UTRs exists for annotation.
`minCDS` | (integer) minimum bp for CDS during filtering for the transcripts
`minThreeUTR` | (integer) minimum bp for 3' UTR during filtering for the transcripts. Set to NULL if no 3' UTRs exists for annotation.
`firstN` | (integer) Represents how many bases of the transcripts downstream of start codons to use for initial estimation of the periodicity.

### Details

For more details, see: `detectRibosomeShifts`

### Value

NULL (Objects are saved to out.dir/pshited/"name")

### See Also

Other pshifting: `changePointAnalysis()`, `detectRibosomeShifts()`, `shiftFootprints()`

[Package ORFik version 1.6.9 Index]