TAPPA {ToPASeq} | R Documentation |
The functions analyses the differential expression of pathways via TAPPA method. Expression is compared between two groups of samples by Mann-Whitney test. P-values are later adjusted for multiple hypothesis testing by Benjamini-Hochberg's FDR method.
TAPPA(x, group, pathways, type, which = "proteins", edgeType = NULL, preparePaths = TRUE, norm.method = NULL, test.method = NULL, test = t.test, normalize = TRUE, verbose = FALSE, both.directions = TRUE, maxNodes = 150, minEdges = 0, commonTh = 2, filterSPIA = FALSE, convertTo = "none", convertBy = NULL)
x |
An |
group |
Name or number of the phenoData column or a character vector or factor that contains required class assigments |
pathways |
A list of pathways in a form from |
type |
Type of the input data, |
which |
Character, which type of nodes is preserved in a pathway. Possible values are |
edgeType |
Character, which type of edges is preserved in a pathway. If |
preparePaths |
Logical, by default the pathways are transformed with |
norm.method |
Character, the method to normalize RNAseq data. If |
test.method |
Character, the method for differentiall expression analysis of RNAseq data. If |
test |
Function implementing a statistical test comparing PCI scores between groups. It is employed as |
normalize |
Logical, should data be normalized? |
verbose |
Logical, if |
both.directions, maxNodes, minEdges, commonTh, filterSPIA, convertTo, convertBy |
Arguments for the |
A list,
res |
A data frame, rows refer to pathways. Columns contain: number of valid PCI-scores, median, min and max of the PCI scores for each group of samples, p-value of the |
topo.sig |
|
degtest |
A numeric vector of gene-level differential expression statistics |
Ivana Ihnatova
Gao, S. and Wang, X. (2007) TAPPA: topological analysis of pathway phenotype association. Bioinformatics, 23, pages 3100-3102
if (require(breastCancerVDX)) { data("vdx") pathways<-pathways("hsapiens","biocarta")[1:10] MAdata<-Biobase::exprs(vdx)[,1:10] rownames(MAdata)<-Biobase::fData(vdx)[,"Gene.symbol"] MAdata<-MAdata[!duplicated(rownames(MAdata)),] TAPPA(MAdata, Biobase::pData(vdx)[,"er"][1:10], pathways, type="MA", convertTo="SYMBOL") }