coverageScorings {ORFik} | R Documentation

## Add a coverage scoring scheme

### Description

Different scorings and groupings of a coverage representation.

### Usage

    coverageScorings(coverage, scoring = "zscore", copy.dt = TRUE)

### Arguments

`coverage` | a data.table containing at least columns (count, position), it is possible to have additionals: (genes, fraction, feature)
`scoring` | a character, one of (zscore, transcriptNormalized, mean, median, sum, log2sum, log10sum, sumLength, meanPos and frameSum, periodic, NULL). More info in details
`copy.dt` | logical TRUE, copy object, to avoid overwriting original object. Set to false to run function using reference to object, a speed up if original object is not needed.

### Details

Usually output of metaWindow or scaledWindowPositions is input in this function.

Content of coverage data.table: It must contain the count and position columns.

genes column: If you have multiple windows, the genes column must define which gene/transcript grouping the different counts belong to. If there is only a meta window or only 1 gene/transcript, then this column is not needed.

fraction column: If you have coverage of i.e RNA-seq and Ribo-seq, or TCP -seq of large and small subunite, divide into fractions. Like factor(RNA, RFP)

feature column: If gene group is subdivided into parts, like gene is transcripts, and feature column can be c(leader, cds, trailer) etc.

Given a data.table coverage of counts, add a scoring scheme. per: the grouping given, if genes is defined, group by per gene in default scoring.
Scorings:

- zscore (count-windowMean)/windowSD per)

- transcriptNormalized (sum(count / sum of counts per))

- mean (mean(count per))

- median (median(count per))

- sum (count per)

- log2sum (count per)

- log10sum (count per)

- sumLength (count per) / number of windows

- meanPos (mean per position per gene) used in scaledWindowPositions

- sumPos (sum per position per gene) used in scaledWindowPositions

- frameSum (sum per frame per gene) used in ORFScore

- frameSumPerL (sum per frame per read length)

- frameSumPerLG (sum per frame per read length per gene)

- fracPos (fraction of counts per position per gene)

- periodic (Fourier transform periodicity of meta coverage per fraction)

- NULL (no grouping, return input directly)

### Value

a data.table with new scores (size dependent on score used)

### See Also

Other coverage: `metaWindow()`, `regionPerReadLength()`, `scaledWindowPositions()`, `windowPerReadLength()`

### Examples

    dt <- data.table::data.table(count = c(4, 1, 1, 4, 2, 3),
                                 position = c(1, 2, 3, 4, 5, 6))
    coverageScorings(dt, scoring = "zscore")

    # with grouping gene
    dt$genes <- c(rep("tx1", 3), rep("tx2", 3))
    coverageScorings(dt, scoring = "zscore")

[Package ORFik version 1.14.7 Index]