write.files: write.files

In mahmoudibrahim/genesorteR: Feature Ranking in Clustered Single Cell Data

Description

write.files saves gene-cluster sorting information obtained from sortGenes to disk.

Usage

write.files(gs, prefix = "genesorteROuts", markers = NULL, eachCluster = FALSE)

Arguments

gs	The output of sortGenes().
prefix	The prefix for saving the files.
markers	Additionally, output files restricted to these genes. A character vector.
eachCluster	Also write individual files for each cluster?

Details

Three files will be saved to disk, including the specificity score matrix, the posterior cluster probability given the gene and the conditional probability of observing the gene in a cluster. If markers is not NULL, three additional files will be created and indicated with "_markers" in their name. If eachCluster is TRUE, additional files (one per cluster will be written which includes all genes and their scaled specificity score for each cluster, with genes sorted by their score.

Author(s)

Mahmoud M Ibrahim <[e-mail]>

Examples

data(sim)
gs = sortGenes(sim$exp, sim$cellType)
## Not run: write.files(gs) #write all files for all genes.
## Not run: write.files(gs, markers = c("g1","g2")) #additionally write files that are restricted to genes g1 and g2.

mahmoudibrahim/genesorteR documentation built on April 20, 2021, 4:07 p.m.