kegg_summary: kegg_summary
In w-korani/keggseq: KEGG analysis and visualizing of differentially expressed genes
Description
Usage
Arguments
Value
Examples
Description
kegg_summary produces a summary table of the
output of calculate_kegg function with including the qvalues.
Usage
1
kegg_summary(dataset)
Arguments
dataset
A output dataset of calculate_kegg.
Value
A data frame containg 7 colums as following:
column1: map_numbers, the map numbers of the KEGG pathway.
column2: pathway_description, the discription the the pathway.
column3: background_gene_numbers, number of all genes
included in the pathway.
column4: deg_gene_numbers, number of
differentially expressed genes in the pathway.
column5: pvalue, p-values of the hypergeometric test for the pathway.
column6: adjusted_pvalue, the Bonferroni method adjustment of p-values.
column7: qvalue, q-values of the pvalues of column5.
Examples
1
2
3
4
5
a <- list_species("arachis")
b <- grep_datasets(c("adu","aip"))
deg_list <- as.matrix(b[b$kegg_pathways=='00061',1])[,1]
c <- calculate_kegg(b,deg_list)
d <- kegg_summary(c)
w-korani/keggseq documentation built on May 3, 2019, 7:10 p.m.
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Description Usage Arguments Value Examples
Description
kegg_summary produces a summary table of the output of calculate_kegg function with including the qvalues.
Usage
1 | kegg_summary(dataset)
|
Arguments
dataset |
A output dataset of calculate_kegg. |
Value
A data frame containg 7 colums as following:
column1: map_numbers, the map numbers of the KEGG pathway.
column2: pathway_description, the discription the the pathway.
column3: background_gene_numbers, number of all genes
included in the pathway.
column4: deg_gene_numbers, number of
differentially expressed genes in the pathway.
column5: pvalue, p-values of the hypergeometric test for the pathway.
column6: adjusted_pvalue, the Bonferroni method adjustment of p-values.
column7: qvalue, q-values of the pvalues of column5.
Examples
1 2 3 4 5 | a <- list_species("arachis")
b <- grep_datasets(c("adu","aip"))
deg_list <- as.matrix(b[b$kegg_pathways=='00061',1])[,1]
c <- calculate_kegg(b,deg_list)
d <- kegg_summary(c)
|
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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