mapStats: mapStats

In charles-plessy/smallCAGEqc: ad-hoc QC functions for shallow-sequenced test CAGE libraries

Description

Process mapping statistics

Usage

mapStats(libs, scope = c("all", "annotation", "counts", "mapped", "qc",
  "steps", "custom"), group = "default", customScope = NULL,
  normalise = TRUE)

Arguments

libs	A data frame with columns named promoter, exon, intron mapped, extracted, rdna, and tagdust.
scope	The value on which to normalise. “all” and “qc” normalise on the number of extracted tags, “annotation” on the number of aligned tags, “mapped” on the number of aligned tags and “counts” on the transcript counts.
group	A vector of factors defining groups in the data. By default, the “group” column of the “libs” table.
customScope	A function that implements a custom scope. Use with scope = "custom". The function takes a data frame in input and returns a named list containing a data frame (“libs”), a character vector of columns to be plotted (“columns”), and a numeric vector of totals for the normalisation (“total”).
normalise	Whether to normalise or not. Default: TRUE.

Details

Using a data frame containing mapping statistics in counts, transform the data in percentages that can be used for stacked barplots.

See http://stackoverflow.com/questions/10417003/stacked-barplot-with-errorbars-using-ggplot2 about stacked barplot.

The “mapped” and “counts” scopes assume that transcript counts are available.

See the plotAnnot vignette for details on what the scopes are.

Value

Returns a data frame with mean and standard deviation of normalised mapping statistics, plus absolute positions for the error bars. The first column, group, is a vector of factors sorted with the gtools::mixedorder function.

See Also

loadLogs, loadMoiraiStats

Other smallCAGEqc annotation functions: hannot, hierarchAnnot, plotAnnot, ranges2annot, ranges2genes

Examples

example(loadMoiraiStats)
mapStats(libs, "qc")

charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.