build.export: Results export builder

In pmoulos/metaseqR: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.

Description

This function help build the output files of the metaseqr pipeline based on several elements produced during the pipeline execution. It is intended for internal use and not available to the users.

Usage

    build.export(gene.data, raw.gene.counts,
        norm.gene.counts, flags, sample.list, cnt, 
        statistics, raw.list, norm.list,
        p.mat = matrix(NA, nrow(gene.data), length(statistics)),
        adj.p.mat = matrix(NA, nrow(gene.data), length(statistics)),
        sum.p = rep(NA, nrow(gene.data)),
        adj.sum.p = rep(NA, nrow(gene.data)),
        export.what = c("annotation", "p.value", "adj.p.value", "meta.p.value", 
                "adj.meta.p.value", "fold.change", "stats", "counts","flags"),
        export.scale = c("natural", "log2", "log10", "rpgm", "vst"),
        export.values = c("raw", "normalized"),
        export.stats = c("mean", "median", "sd", "mad", "cv", "rcv"),
        log.offset = 1, report = TRUE)

Arguments

gene.data	an annotation data frame (such the ones produced by get.annotation).
raw.gene.counts	a matrix of filtering flags (0,1), created by the filtering functions.
norm.gene.counts	a matrix of normalized gene counts.
flags	a matrix of normalized gene counts.
sample.list	see the documentation of metaseqr.
cnt	the statistical contrast for which the export builder is currently running.
statistics	the statistical tests used (see the documentation of metaseqr).
raw.list	a list of transformed un-normalized counts, see the documentation of make.transformation.
norm.list	a list of transformed normalized counts, see the documentation of make.transformation.
p.mat	a matrix of p-values, see the documentation of metaseqr.
adj.p.mat	a matrix of adjusted p-values, see the documentation of metaseqr.
sum.p	a vector of combined p-values, see the documentation of metaseqr.
adj.sum.p	a vector of adjusted combined p-values, see the documentation of metaseqr.
export.what	see the documentation of metaseqr.
export.scale	see the documentation of metaseqr.
export.values	see the documentation of metaseqr.
export.stats	see the documentation of metaseqr.
log.offset	see the documentation of metaseqr.
report	see the documentation of metaseqr.

Value

A list with three members: a data frame to be exported in a text file, a long string with the result in a html formatted table (if report=TRUE) and the column names of the output data frame.

Author(s)

Panagiotis Moulos

Examples

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pmoulos/metaseqR documentation built on Dec. 21, 2020, 6:19 a.m.