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

In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

Description

Each tab in the summary spreadsheet of the

Usage

	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

## 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: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

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

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package: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: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid


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

Attaching package: ‘Matrix’

The following object is masked from ‘package:S4Vectors’:

    expand

Loading required package: graph

Attaching package: ‘GOstats’

The following object is masked from ‘package: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.