RUN_GSAA: RUN_GSAA
In ChristophRau/GSAA: Gene Set Association Analysis
RUN_GSAA R Documentation
RUN_GSAA
Description
Master Function for running GSAA.
Usage
RUN_GSAA(input,ensembl_dataset="mmusculus_gene_ensembl",mart="illumina_mouseref_8_v2",GO_Member_Threshold=10,qval_threshold=.05)
Arguments
input
matrix with gene names as column names, group names as row names, and strengths as entries
ensembl_dataset
Which biomart will be used. Species Specific.
mart
which specific dataset within the biomart will be used. Platform Specific.
GO_Member_Threshold
Threshold for eliminating GO Terms with fewer than this many members from the incidence table (equivalent to a Minor Allele Frequency Filter in a GWAS)
qval_threshold
FDR threshold for significance. Will take either 0-1 or 0-100 as inputs
Value
Incidence_Table
The Incidence_Table of genes and GO Terms (equivalent to a genotype file in GWAS)
Sig_Results
Significant GSAA results
Author(s)
Christoph Rau
See Also
GSAA,calculateIncidenceTable
ChristophRau/GSAA documentation built on March 2, 2023, 5:29 a.m.
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| RUN_GSAA | R Documentation |
RUN_GSAA
Description
Master Function for running GSAA.
Usage
RUN_GSAA(input,ensembl_dataset="mmusculus_gene_ensembl",mart="illumina_mouseref_8_v2",GO_Member_Threshold=10,qval_threshold=.05)
Arguments
input |
matrix with gene names as column names, group names as row names, and strengths as entries |
ensembl_dataset |
Which biomart will be used. Species Specific. |
mart |
which specific dataset within the biomart will be used. Platform Specific. |
GO_Member_Threshold |
Threshold for eliminating GO Terms with fewer than this many members from the incidence table (equivalent to a Minor Allele Frequency Filter in a GWAS) |
qval_threshold |
FDR threshold for significance. Will take either 0-1 or 0-100 as inputs |
Value
Incidence_Table |
The Incidence_Table of genes and GO Terms (equivalent to a genotype file in GWAS) |
Sig_Results |
Significant GSAA results |
Author(s)
Christoph Rau
See Also
GSAA,calculateIncidenceTable
R Package Documentation
Browse R Packages
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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