re: Random Effects Heterogeneity Analysis.

Description Usage Arguments Specifying The Input Data Files Specifying Column Names in Input Data Files Field Separator in Input Data Files Case Sensitivity Output File Name Author(s)

Description

Outlier cohorts detection in meta-analysis based on random effects.

Usage

1
re(script)

Arguments

script

Name of a textual input file with processing instructions. The file should contain the names and locations of all GWAS data files to be processed along with basic information from each individual study.

Specifying The Input Data Files

The names of the GWAS data files are specified in the input script with the command PROCESS (one line per file). A different directory path can be specified for each file.

Example:

PROCESS input_file_1.txt
PROCESS /dir_1/dir_2/input_file_2.csv

The annotation is applied first to ‘input_file_1.txt’ and then to ‘input_file_2.csv’.

Specifying Column Names in Input Data Files

In the table below, the complete list of the default column names for the GWAS data file is reported. These names identify uniquely the items in the GWAS data file.

Default column name(s) Description
MARKER Marker name
CHR Chromosome number or name
POSITION Marker position

Given that different names can be provided for each GWAS data file, annotate() allows to redefine the default values for every input file in the input script. The redefinition command consists of the default column name followed by the new column name. When the map file is specified using command MAP_FILE, then CHR and POSITION columns in the GWAS data file are not required.

Example:

Let's assume to have two input files, ‘input_file_1.txt’ and ‘input_file_2.csv’. In the ‘input_file_1.txt’, the column names for marker name, chromosome name and position are SNPID, CHR and POS, respectively. In the ‘input_file_2.csv’, the column names for marker name is the same as in ‘input_file_1.txt’, but the column names for the chromosome and position are chromosome and position, respectively. The correct column redefinition is as follows:

MARKER SNPID
POSITION POS
PROCESS input_file_1.txt
CHR chromosome
POSITION position
PROCESS input_file_2.csv

There are no need to define the CHR field for the ‘input_file_1.txt’, since it matches the default name.

Field Separator in Input Data Files

The field (column) separator can be different for each GWAS data file. annotate() automatically detects the original separator field for each input file based on the first 10 rows. However, the user has the possibility to specify the original separator manually for each individual file using the command SEPARATOR. The supported arguments and related separators are listed below:

Argument Separator
COMMA comma
TAB tabulation
WHITESPACE whitespace
SEMICOLON semicolon

Example:

PROCESS input_file_1.txt
SEPARATOR COMMA
PROCESS input_file_2.csv
PROCESS input_file_3.txt

For the input file ‘input_file_1.txt’ the field separator is determined automatically by the program but, for the input files ‘input_file_2.csv’ and ‘input_file_3.txt’ the separator is manually set to comma by the user.

Case Sensitivity

By default the annotate() assumes that column names in the all specified files are case insensitive. For example, the column names CHR, Chr, and chr are all perfectly equivalent. This behaviour can be modified for every input file in the input script using the command CASESENSITIVE, that controls case sensitivity for the column names, as specified below:

Argument Description
0 Column names in the input file
are case insensitive (default)
1 Column names in the input file
are case sensitive

Example:

CASESENSITIVE 1
MAP_FILE map_file_1.txt
REGIONS_FILE genes_file_1.txt
PROCESS input_file_1.txt
CASESENSITIVE 0
MAP_FILE map_file_2.csv
REGIONS_FILE genes_file_2.csv
PROCESS input_file_2.csv

Output File Name

The output file names are created by adding a prefix to the input file names. The prefix is specified with the command PREFIX.

Example:

REGIONS_FILE genes_file_1.txt
PREFIX annotated_
PROCESS input_file_1.txt
PROCESS input_file_2.csv
PREFIX annot_
PROCESS input_file_3.tab

All the output files corresponding to the input files ‘input_file_1.txt’ and ‘input_file_2.csv’ will be prefixed with annotated_; the output files corresponding to the input file ‘input_file_3.tab’ will be prefixed with annot_.

Author(s)

Daniel Taliun, Christian Fuchsberger, Cristian Pattaro


GWAtoolbox documentation built on May 2, 2019, 4:54 p.m.