Description Usage Arguments Examples
find_optimal_cluster_number identifies the optimal number of initial cluster number by searching from min_cluster_num to max_cluster_num
1 2 | find_optimal_cluster_number(rpkmFile, sampleFile, min_cluster_num = 7,
max_cluster_num = 13, diversity_cut = 0.6, size_cut = 0.05)
|
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. |
1 2 3 4 5 6 7 8 9 | ## 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)
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