pipe.MetaResults | R Documentation |
Top level wrapper function to call a family of published DE tools, that each find significant differentially expressed genes between groups of samples, and then after all DE tools complete, combine and merge all separate DE results into one folder of Meta Results.
pipe.MetaResults(sampleIDset, speciesID = getCurrentSpecies(), annotationFile = "Annotation.txt",
optionsFile = "Options.txt", useMultiHits = TRUE, results.path = NULL,
folderName = "", groupColumn = "Group", colorColumn = "Color",
average.FUN = sqrtmean, tools = c("RoundRobin", "RankProduct", "SAM", "EdgeR", "DESeq"),
altGeneMap = NULL, altGeneMapLabel = NULL, targetID = NULL, Ngenes = 100,
geneColumnHTML = if (speciesID %in% MAMMAL_SPECIES) "NAME" else "GENE_ID",
keepIntergenics = FALSE, verbose = TRUE, label = "", doDE = TRUE,
makePlots = doDE, copyPlots = makePlots, nFDRsimulations = 0,
addCellTypes = (speciesID %in% MAMMAL_SPECIES),
addLifeCycle = (speciesID %in% PARASITE_SPECIES), PLOT.FUN = NULL, ...)
sampleIDset |
Character vector of SampleIDs, giving the full set of samples that will take part in the DE calculations. |
speciesID |
The SpeciesID for one single species. The DE tools do not operate on multipe species at one time. |
annotationFile |
File of sample annotation details, which specifies all needed
sample-specific information about the samples under study.
See |
optionsFile |
File of processing options, which specifies all processing
parameters that are not sample specific. See |
useMultiHits |
Logical. By default, all DE tools use the RPKM or READ values from the transcriptomes that correspond
to keeping all aligned reads, including those alignments called "MultiHit" reads. If |
results.path |
The top level folder path for writing result files to. By default, read from the Options file entry 'results.path'. |
folderName |
Required character string, with no embedded blanks, used to name the folder of DE results that will be generated by the DE tool. Typically, use a short but informative name that describes the groups being compared. |
groupColumn |
Character string specifying one column of the annotation table, to give the group name for each sample. |
colorColumn |
Character string specifying one column of the annotation table, to give the group color for each sample. |
average.FUN |
The function to use for taking the average value of gene ranks across the 5 DE results. Passed down to
|
tools |
Character vector of which DE tools to use. Defaults to all 5 currently implemented. |
altGeneMap |
An alternate data frame of gene annotations, in a format identical to |
altGeneMapLabel |
A character string identifier for the alternate gene map, that becomes part of all created path and file names to indicate the gene map that produced the transcriptomes used in this DE analysis. |
targetID |
Optional character string giving the target organism(s) being compared. Used by the gene plotting tools, defaults to the current target. |
Ngenes |
Number of gene to show in the HTML results and create gene plot images for. |
geneColumnHTML |
The name of one column in the current gene map, that contains the identifier shown in the HTML results. Some genomes require complex compound GeneIDs to give genomic location specificity, but are unwieldy for routine use. This argument lets a second simpler identifier be used as a surrogate GeneID. |
keepIntergenics |
Logical. By default, all transcriptomes keep gene expression values for defined intergenic "non-gene" regions defined in the gene map. These intergenic regions can be included or excluded from the DE fold change comparisons and results. |
label |
A character string that is passed to the gene plot tool, for inclusion in the main plot header. |
doDE |
Logical, controls whether the complete DE analysis is performed, or whether to just use results already present in the DE subfolder. When FALSE, do not dispatch any DE tools, just do the final meta results combination steps. |
makePlots |
Logical, should the dispatched DE tools make plots or not. |
copyPlots |
Logical, should the final meta results step copy over plots from the dispatched DE tools. |
nFDRsimulations |
Passed down to |
addCellTypes |
Logical, controls the addition of additional data columns and result files that associate a immune cell subset call to each gene, and then estimate cell subset enrichment for each DE group. Only currently applicable for mammalian genomes. |
addLifeCycle |
Logical, controls the addition of additional data columns and result files that associate a parasite lifecycle stage call to each gene, and then estimate lifecycle stage enrichment for each DE group. Only currently applicable for parasite genomes. |
PLOT.FUN |
An alternative function to use for generating gene plot images, that accepts a single GeneID as its
argument. Use |
... |
Other arguments passed down the to gene plotting function. |
This pipe acts as a top level DE tool, dispatching independent DE tools with differing methods, and then merging and averaging all those results into a final meta DE result.
The grouping column from the annotation file determines: how the samples are combined into groups, the names for all result files, and the number of different groups being compared. When more than 2 groups are being compared, a K-ways comparison is performed such that each one group is compared against all other groups combined, like a "Us against all other groups who are not us" strategy.
Each comparison creates a family of result files, with suffix names "UP" and "DOWN", to convey the
direction of each comparison. Note that in the case of just 2 groups, the UP and DOWN results are
roughly symmetric, but that is never true for 3+ group comparisons. Each comparison file uses a
composite naming strategy combining <Group>.<Species>.Meta.<DirectionSuffix>
.
A subfolder of result files, with a name constructed from the current species prefix and folderName
.
For each group name, a set of DE result files in various formats:
UP.txt |
|
DOWN.txt |
Tab delimited files of all genes in the species, sorted by average fold-change, average P-value, and average rank, across all the DE tooks, and includes extra columns showing the actual gene rank position in each DE tool. |
UP.html |
|
DOWN.html |
A pair of HTML files of gene expression showing just the top |
Cluster & PCA |
A set of .PNG plots that visually summarize the similarity of the transcriptsomes, augmented with "group average" transcriptomes as well. |
Enrichment.csv |
Optional CSV files of gene subset enrichment, by cell type or life cycle stage |
By default, the function invokes multicore parallel processing to run the 5 DE tools at the same time.
As such, all DE tools are writing their status to standard out at the same time, making it very hard to
catch any runtime error messages. If an unexpected error occurs, turn off multicore behavior with
multicore.setup(1)
and rerun. The true error cause should now be more easy to deduce.
Bob Morrison
pipe.MetaGeneSets
for dispatching all Gene Set & Pathway tools and merging their results.
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