Description Usage Arguments Details Value See Also Examples
Process mapping statistics
1 2 3 |
libs |
A data frame with columns named |
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
|
normalise |
Whether to normalise or not. Default: TRUE. |
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.
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.
Other smallCAGEqc annotation functions: hannot
,
hierarchAnnot
, plotAnnot
,
ranges2annot
, ranges2genes
1 2 | example(loadMoiraiStats)
mapStats(libs, "qc")
|
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