top.genes: Top Variable Gene Identificaiton
In morris-lab/Capybara: A tool to measure cell identity and fate transitions
View source: R/SingleCellQuadraticProgrammingAux.R
top.genes R Documentation
Top Variable Gene Identificaiton
Description
This function identifies top n variable genes using method described in KeyGenes algorithm. In brief, this algorithm use cross validation based on LASSO regression. For detailed explanation, please refer to the paper listed in the note.
Usage
top.genes(input.dir, output.dir, top.number.count = 500)
Arguments
input.dir
The path to where the dataset is saved. Dataset should be saved as a tab-delimited table with row = gene, column = cell.
output.dir
The path to where the output should be saved. The output will be saved as a tab-delimited table with NO row names or column names.
top.number.count
The number of top variable genes to extract. Default to 500 genes
Note
Code reference from Roost et. al., KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas, Cell Stem Cell Reports, 2015
Examples
top.genes("~/Desktop/sample_data.txt", "~/Desktop/sample_gene_list_output.txt", top.number.count = 1000)
morris-lab/Capybara documentation built on June 13, 2022, 10:33 p.m.
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View source: R/SingleCellQuadraticProgrammingAux.R
| top.genes | R Documentation |
Top Variable Gene Identificaiton
Description
This function identifies top n variable genes using method described in KeyGenes algorithm. In brief, this algorithm use cross validation based on LASSO regression. For detailed explanation, please refer to the paper listed in the note.
Usage
top.genes(input.dir, output.dir, top.number.count = 500)
Arguments
input.dir |
The path to where the dataset is saved. Dataset should be saved as a tab-delimited table with row = gene, column = cell. |
output.dir |
The path to where the output should be saved. The output will be saved as a tab-delimited table with NO row names or column names. |
top.number.count |
The number of top variable genes to extract. Default to 500 genes |
Note
Code reference from Roost et. al., KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas, Cell Stem Cell Reports, 2015
Examples
top.genes("~/Desktop/sample_data.txt", "~/Desktop/sample_gene_list_output.txt", top.number.count = 1000)
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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