find_optimal_cluster_number: find_optimal_cluster_number identifies the optimal number of...

Description Usage Arguments Examples

View source: R/Mpath.R

Description

find_optimal_cluster_number identifies the optimal number of initial cluster number by searching from min_cluster_num to max_cluster_num

Usage

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find_optimal_cluster_number(rpkmFile, sampleFile, min_cluster_num = 7,
  max_cluster_num = 13, diversity_cut = 0.6, size_cut = 0.05)

Arguments

rpkmFile

a tab delimited txt file of expression data, containing cells in columns and genes in rows

sampleFile

a tab delimited txt file of sample annotation with two columns, the first column is cell ID, the second column is group ID

min_cluster_num

minimum number of initial clusters

max_cluster_num

maximum number of initial clusters

diversity_cut

the cutoff value of diversity for differentiating landmark clusters from non-landmark clusters. The diversity of a landmark cluster must be below this cutoff.

size_cut

the cutoff value of size i.e. number of cells for differentiating landmark clusters from non-landmark clusters. The number of cells in a landmark cluster must be greater than this cutoff.

Examples

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## Not run: 
rpkmFile = "TPM_GSE60783_noOutlier_geneQC0.05anyGroup_CD4vsCD8DEG.txt";
sampleFile = "sample_GSE60783_noOutlier.txt";
find_optimal_cluster_number(rpkmFile = rpkmFile,
                            sampleFile = sampleFile,
                            min_cluster_num = 7, max_cluster_num = 15,
                            diversity_cut = 0.6, size_cut = 0.05)

## End(Not run)

Zouter/MPath_gh documentation built on May 14, 2019, 8:58 a.m.