metaseqR (version 1.12.2)

build.export: Results export builder

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.

Examples

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