Skip to content

Latest commit

 

History

History
33 lines (23 loc) · 1.58 KB

burdenshift.rst

File metadata and controls

33 lines (23 loc) · 1.58 KB
Raw

Burden shift analysis

From burden test results, CWAS-Plus can find overrepresented domains across significant categories. By comparing the observed number of significant categories with the number of significant categories from samples with a randomly shuffled phenotype, the significance of the overrepresentation is determined.

The parameters of the command are as below:

  • -i, --input_file: Path to the input file which is the result of binomial burden test (*.burden_test.txt).
  • -b, --burden_res: Path to the result of burden shift from permutation test (*.binom_pvals.txt.gz).
  • -c_info, --category_info: Path to a text file with category information (*.category_info.txt).
  • -o_dir, --output_directory: Path to the directory where the output files will be saved. By default, outputs will be saved at $CWAS_WORKSPACE.
  • -c_set, --cat_set: Path to the category information file from binomial burden test (*.category_info.txt).
  • -c_count, --cat_count: Path of the categories counts file from binomial burden test (*.category_counts.txt).
  • -t, --tag: Tag used for the name of the output files. By default, None.
  • -c_cutoff, --count_cutoff: The number of cutoff for category counts. It must be positive value. By default, 7.
  • --pval: P-value threshold. By default, 0.05.
cwas burden_shift -i INPUT.burden_test.txt \
-b INPUT.binom_pvals.txt.gz \
-o_dir OUTPUT_DIR \
-c_info INPUT.category_info.txt \
-c_count INPUT.category_counts.txt \
-c_cutoff 7 \
--pval 0.05