printSummary: Function to print the summary file of PloGO2 results.

Description Usage Arguments Value Author(s) Examples

View source: R/printSummary.R

Description

Each tab in the summary spreadsheet of the

Usage

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	printSummary(results, file="PloGO2Results.xlsx") 

Arguments

results

A list of results from PloGO2 analysis

file

The output file name

Value

TRUE if at least some annotations were found, FALSE otherwise.

Author(s)

J. Wu

Examples

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## Not run: 
path <- system.file("files", package = "PloGO2")
# run PloPathway with list of id's, data file and reference
res <- PloPathway( zipFile=paste(path, "PWFiles.zip", sep="/"), 
	reference="Alldata", 
	data.file.name = paste(path, "Abundance_data.csv", sep="/"),
	datafile.ignore.cols = 1)

printSummary(res)

## End(Not run)

Example output

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package:BiocGenericsThe following objects are masked frompackage:parallel:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage:base:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package:S4VectorsThe following object is masked frompackage:base:

    expand.grid


Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix

Attaching package:MatrixThe following object is masked frompackage:S4Vectors:

    expand

Loading required package: graph

Attaching package:GOstatsThe following object is masked frompackage:AnnotationDbi:

    makeGOGraph

/work/tmp/tmp/Rtmp8Hevqp/AllData.txt /work/tmp/tmp/Rtmp8Hevqp/black.txt /work/tmp/tmp/Rtmp8Hevqp/blue.txt /work/tmp/tmp/Rtmp8Hevqp/brown.txt /work/tmp/tmp/Rtmp8Hevqp/green.txt /work/tmp/tmp/Rtmp8Hevqp/red.txt /work/tmp/tmp/Rtmp8Hevqp/turquoise.txt /work/tmp/tmp/Rtmp8Hevqp/yellow.txt

PloGO2 documentation built on Nov. 8, 2020, 5:40 p.m.