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)
Outlier cohorts detection in meta-analysis based on random effects.
1 | re(script)
|
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. |
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’.
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.
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.
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 |
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_.
Daniel Taliun, Christian Fuchsberger, Cristian Pattaro
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