build.export {metaseqR} | R Documentation

## 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.

### Author(s)

Panagiotis Moulos

### Examples

    ## Not run:
    # Not yet available

    ## End(Not run)

[Package metaseqR version 1.26.0 Index]