AlvMac_results.pVal: Sample output from the 'pValue_GO()' function on an RNAseq...

In kevinrue/GOexpress-original: Visualise microarray and RNAseq data using gene ontology annotations

Description

This variable may be used to test the filtering and visualisation methods implemented in the package. It contains the output of successively applying the commands AlvMac_results = GO_analyse(eSet=AlvMac, f="Treatment") and AlvMac_results.pVal = pValue_GO(AlvMac_results, N=100, ranked.by=result$rank.by, rank.by='P') to the toy input data AlvMac.

Usage

data("AlvMac_results.pVal")

Value

A list of 9 slots summarising the input and results of the analysis:

• GO contains a table ranking all GO terms related to genes in the expression dataset based on the average ability of their related genes to cluster the samples according to the predefined grouping factor.

• mapping contains the table mapping genes present in the dataset to GO terms.

• genes contains a table ranking all genes present in the expression dataset based on their ability to cluster the samples according to the predefined grouping factor (see 'factor' below).

• factor contains the grouping factor analysed.

• method contains the statistical framework used.

• subset contains the filters used to select a subset of samples from the original ExpressionSet for analysis.

• rank.by contains the metric used to rank the scoring tables.

• ntree contains number of trees built during the randomForest analysis.

• mtry contains the number of features randomly sampled as candidates at each split in each tree built during the randomForest analysis.

• p.iterations contains the number of permutations performed to compute the P-value in the GO slot.

Warning

Running the above command again, you might obtain slightly different scores and ranks due to the stochastic process of sampling used by the random forest algorithm. However, the ranking metric was found to be robust and stable across run, given adequate number of trees and predictor variables sampled.

To produce reproducible results, use the set.seed() function prior to running any randomising or sampling function.

Source

Source data are part of a publication in review.

Examples

data(AlvMac_results.pVal)
str(AlvMac_results.pVal)
head(AlvMac_results.pVal, n=20)

kevinrue/GOexpress-original documentation built on May 20, 2019, 9:07 a.m.