Outlier Analysis

Outlier analysis module to identify aberrantly highly expressed genes. Takes in a Gene(rows) X Sample(columns) matrix and identifies genes that have outlier expression in the cohort

Usage

Rscript --vanilla outlier.R -l gene_list -m gene_matrix -o output_directory Rscript --vanilla outlier_scaled.R -l gene_list -m gene_matrix -o output_directory

using example files

Rscript --vanilla outlier.R -l gene_list_example.txt -m gene_matrix_example.tsv -o out

with log transformation

Rscript --vanilla outlier.R -l gene_list_example.txt -m gene_matrix_example.tsv -t -o out

with outlier score cut-off: default 1.5

Rscript --vanilla outlier.R -l gene_list_example.txt -m gene_matrix_example.tsv -o out -c 1.5