vtools_report meta_analysis implements meta-analysis methods detailed in (Willer et al, 2010). Two statistics are available: the sample size based statistic and inverse variance based statistic. Input of this command are multiple text or compressed text files of association results delimited by tabs.
% vtools_report meta_analysis -h
usage: vtools_report meta_analysis [-h] [--beta col] [--pval col] [--se col]
[-n col] [--link col [col ...]] [-m method]
[--to_db database] [-v {0,1,2}]
file [file ...]
positional arguments:
file Input text files in the format of \\(vtools associate
output (supports plain text, gz or bz2 compressed text
files)
optional arguments:
-h, --help show this help message and exit
--beta col column number of beta
--pval col column number of p-value
--se col column number of standard error
-n col, --size col column number of sample size
--link col [col ...] columns that links entries of two datasets
-m method, --method method
Method (choose from "ssb" for sample based method and
"ivb" for inverse variance based method), default set
to "ssb"
--to_db database will write the results also to a sqlite3 database
compatible with vtools associate result format
-v {0,1,2}, --verbosity {0,1,2}
Output error and warning (0), info (1) and debug (2)
information of vtools and vtools_report. Debug
information are always recorded in project and
vtools_report log files.
Input files are
% zless study1.gz
refGene_name2 sample_size_VT num_variants_VT total_mac_VT beta_x_VT pvalue_VT std_error_VT num_permutations_VT MAF_threshold_VT
A1BG 159 2 24 0.0191151 0.891109 0.213265 1000 0.00628931
A1BG-AS1 309 2 43 -0.409899 0.563437 0.27416 1000 0.00161812
A1CF 327 6 10 0.274825 0.275724 0.18807 1000 0.00152905
A2M 330 6 21 -0.0123306 0.985015 0.153102 1000 0.00151515
A2ML1 331 8 19 -0.280548 0.25974 0.159701 1000 0.00151057
...
study2.gz is in the same format. The effect size is the 5th column, p-value the 6th column and sample size 1st column. The two data-sets are matched by gene name, i.e., the first column. The meta analysis command is:
% vtools_report meta_analysis study1.gz study2.gz --beta 5 --pval 6 --size 2 --link 1 \
% --to_db study1and2 > study1and2.txt
Result are outputted to both text file and database.
% less study1and2.txt
refGene_name2 p_meta sample_size_meta beta_x_VT_1 pvalue_VT_1 sample_size_VT_1 beta_x_VT_2 pvalue_VT_2 sample_size_VT_2
RESP18 6.380E-01 238 0.570054 0.1998 119 -0.228113 0.537463 119
STX6 8.583E-01 633 0.010475 0.875125 302 -0.434853 0.691309 331
ARFGEF2 7.984E-01 645 0.161718 0.417582 314 -0.169275 0.251748 331
TSEN34 3.459E-01 104 0.604153 0.323676 52 0.461471 0.729271 52
...
To load the meta analysis result to the project
% vtools use study1and2.DB --linked_by name2
INFO: Using annotation DB study1and2 in project SSc.
INFO: Combined association tests result database. Created on Thu, 14 Mar 2013 17:35:44
INFO: 7459 out of 23242 refGene.name2 are annotated through annotation database study1and2
C. J. Willer, Y. Li and G. R. Abecasis (2010). METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics