Provided by: libgenome-model-tools-music-perl_0.04-4_all 
genome music clinical-correlation
NAME
genome music clinical-correlation - Correlate phenotypic traits against mutated genes, or against
individual variants
VERSION
This document describes genome music clinical-correlation version 0.04 (2018-07-05 at 09:17:13)
SYNOPSIS
genome music clinical-correlation --bam-list=? --output-file=? [--maf-file=?]
[--glm-clinical-data-file=?] [--use-maf-in-glm] [--skip-non-coding] [--skip-silent]
[--clinical-correlation-matrix-file=?] [--input-clinical-correlation-matrix-file=?]
[--genetic-data-type=?] [--numeric-clinical-data-file=?] [--numerical-data-test-method=?]
[--categorical-clinical-data-file=?] [--glm-model-file=?]
... music clinical-correlation \
--bam-list /path/myBamList.tsv \
--maf-file /path/myMAF.tsv \
--numeric-clinical-data-file /path/myNumericData.tsv \
--genetic-data-type 'gene' \
--output-file /path/output_file
... music clinical-correlation \
--maf-file /path/myMAF.tsv \
--bam-list /path/myBamList.tsv \
--numeric-clinical-data-file /path/myNumericData.tsv \
--categorical-clinical-data-file /path/myClassData.tsv \
--genetic-data-type 'gene' \
--output-file /path/output_file
... music clinical-correlation \
--maf-file /path/myMAF.tsv \
--bam-list /path/myBamList.tsv \
--output-file /path/output_file \
--glm-model-file /path/model.tsv \
--glm-clinical-data-file /path/glm_clinical_data.tsv \
--use-maf-in-glm
REQUIRED ARGUMENTS
bam-list Text
Tab delimited list of BAM files [sample_name, normal_bam, tumor_bam] (See Description)
output-file Text
Results of clinical-correlation tool. Will have suffix added for data type
OPTIONAL ARGUMENTS
maf-file Text
List of mutations using TCGA MAF specification v2.3
glm-clinical-data-file Text
Clinical traits, mutational profiles, other mixed clinical data (See DESCRIPTION)
use-maf-in-glm Boolean
Create a variant matrix from the MAF file as variant input to GLM analysis.
Default value 'false' (--nouse-maf-in-glm) if not specified
nouse-maf-in-glm Boolean
Make use-maf-in-glm 'false'
skip-non-coding Boolean
Skip non-coding mutations from the provided MAF file
Default value 'true' if not specified
noskip-non-coding Boolean
Make skip-non-coding 'false'
skip-silent Boolean
Skip silent mutations from the provided MAF file
Default value 'true' if not specified
noskip-silent Boolean
Make skip-silent 'false'
clinical-correlation-matrix-file Text
Specify a file to store the sample-vs-gene matrix created during calculations
input-clinical-correlation-matrix-file Text
Instead of creating this from the MAF, input the sample-vs-gene matrix for calculations
genetic-data-type Text
Correlate clinical data to "gene" or "variant" level data
Default value 'gene' if not specified
numeric-clinical-data-file Text
Table of samples (y) vs. numeric clinical data category (x)
numerical-data-test-method Text
Either 'cor' for Pearson Correlation or 'wilcox' for the Wilcoxon Rank-Sum Test for numerical
clinical data
Default value 'cor' if not specified
categorical-clinical-data-file Text
Table of samples (y) vs. categorical clinical data category (x)
glm-model-file Text
File outlining the type of model, response variable, covariants, etc. for the GLM analysis. (See
DESCRIPTION)
DESCRIPTION
This command relates clinical traits and mutational data. Either one can perform correlation analysis
between mutations recorded in a MAF and the particular phenotypic traits recorded in clinical data files
for the same samples, or one can run a generalized linear model (GLM) analysis on the same types of data.
The clinical data files for correlation must be separated between numeric and categoric data and must
follow these conventions:
• Headers are required
• Each file must include at least 1 sample_id column and 1 attribute column, with the format being
[sample_id clinical_data_attribute_1 clinical_data_attribute_2 ...]
• The sample ID must match the sample ID listed in the MAF under "Tumor_Sample_Barcode" for relating
the mutations of this sample.
Note the importance of the headers: the header for each clinical_data_attribute will appear in the output
file to denote relationships with the mutation data from the MAF.
Internally, the input data is fed into an R script which calculates a P-value representing the
probability that the correlation seen between the mutations in each gene (or variant) and each phenotype
trait are random. Lower P-values indicate lower randomness, or likely true correlations.
The results are saved to the output filename given with a suffix appended; ".numeric.csv" will be
appended for results derived from numeric clinical data, and ".categorical.csv" will be appended for
results derived from categorical clinical data. Also, ".glm.csv" will be appended to the output filename
for GLM results.
The GLM analysis accepts a mixed numeric and categoric clinical data file, input using the parameter
--glm-clinical-data-file. GLM clinical data must adhere to the formats described above for the
correlation clinical data files. GLM also requires the user to input a --glm-model-file. This file
requires specific headers and defines the analysis to be performed rather exactly. Here are the
conventions required for this file:
• Columns must be ordered as such:
• [ analysis_type clinical_data_trait_name variant/gene_name covariates memo ]
• The 'analysis_type' column must contain either "Q", indicating a quantative trait, or "B", indicating
a binary trait will be examined.
• The 'clinical_data_trait_name' is the name of a clinical data trait defined by being a header in the
--glm-clinical-data-file.
• The 'variant/gene_name' can either be the name of one or more columns from the
--glm-clinical-data-file, or the name of one or more mutated gene names from the MAF, separated by
"|". If this column is left blank, or instead contains "NA", then each column from either the variant
mutation matrix (--use-maf-in-glm) or alternatively the --glm-clinical-data-file is used
consecutively as the variant column in independent analyses.
• 'covariates' are the names of one or more columns from the --glm-clinical-data-file, separated by
"+".
• 'memo' is any note deemed useful to the user. It will be printed in the output data file for
reference.
GLM analysis may be performed using solely the data input into --glm-clinical-data-file, as described
above, or alternatively, mutational data from the MAF may be included as variants in the GLM analysis, as
also described above. Use the --use-maf-in-glm flag to include the mutation matrix derived from the maf
as variant data.
Note that all input files for both correlation and GLM analysis must be tab-separated.
ARGUMENTS
--bam-list
Provide a file containing sample names and normal/tumor BAM locations for each. Use the tab-
delimited format [sample_name normal_bam tumor_bam] per line. This tool only needs sample_name, so
all other columns can be skipped. The sample_name must be the same as the tumor sample names used in
the MAF file (16th column, with the header Tumor_Sample_Barcode).
LICENSE
Copyright (C) 2010-2011 Washington University in St. Louis.
It is released under the Lesser GNU Public License (LGPL) version 3. See the associated LICENSE file in
this distribution.
AUTHORS
Nathan D. Dees, Ph.D.
Qunyuan Zhang, Ph.D.
William Schierding, M.S.
SEE ALSO
genome-music(1), genome(1)