getPValue: Calculate p-value and adjust p-value of KEGG pathway on input...
In ppdragondw/Key2Enrich: R package of gene set enrichment analysis
Description
Usage
Arguments
Value
Examples
Description
Calculate p-value and adjust p-value of KEGG pathway on input sample
Usage
1
getPValue(thispathwayID_DF, thisKEGGSpecies, thisInputSampleKEGG, N, n)
Arguments
thispathwayID_DF
KEGG pathway ID
thisKEGGSpecies
species in KEGG format
thisInputSampleKEGG
input sample with in KEGG gene ID
N
the number of all genes with KEGG gene ID
n
the number of sample genes with KEGG gene ID
Value
vector in dataframe class containing p-value, adjust p-value,
N:the number of all genes with KEGG gene ID,
n the number of sample genes with KEGG gene ID,
M:the number of all genes in specific KEGG pathway,
m: the number of sample genes in specific KEGG pathway
Examples
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data(inputSample)
inputSample<-as.data.frame(inputSample)
allGeneInPathwayDF<-getAllGeneInPathwayDF("mmu")
N<-getN(allGeneInPathwayDF)
n<-get_n(inputSample,allGeneInPathwayDF)
getPValue("mmu00053","mmu",inputSample,N,n)
ppdragondw/Key2Enrich documentation built on May 29, 2019, 7:39 a.m.
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Description Usage Arguments Value Examples
Description
Calculate p-value and adjust p-value of KEGG pathway on input sample
Usage
1 | getPValue(thispathwayID_DF, thisKEGGSpecies, thisInputSampleKEGG, N, n)
|
Arguments
thispathwayID_DF |
KEGG pathway ID |
thisKEGGSpecies |
species in KEGG format |
thisInputSampleKEGG |
input sample with in KEGG gene ID |
N |
the number of all genes with KEGG gene ID |
n |
the number of sample genes with KEGG gene ID |
Value
vector in dataframe class containing p-value, adjust p-value, N:the number of all genes with KEGG gene ID, n the number of sample genes with KEGG gene ID, M:the number of all genes in specific KEGG pathway, m: the number of sample genes in specific KEGG pathway
Examples
1 2 3 4 5 6 7 | data(inputSample)
inputSample<-as.data.frame(inputSample)
allGeneInPathwayDF<-getAllGeneInPathwayDF("mmu")
N<-getN(allGeneInPathwayDF)
n<-get_n(inputSample,allGeneInPathwayDF)
getPValue("mmu00053","mmu",inputSample,N,n)
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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