Output control options

• Analysis summary
  • Export result with different format
  • Remove NAs from the output file
  • Filter variants of which p-values are in certain range
  • Report computing time for each test
• Annotation summary
  • Using pre-defined annotation file
  • Annotate variants with each gene
  • Expading annotation range
  • Analyses supporting annotation functions

Analysis summary [top]

Export result with different format

From version 1.1.1, WISARD exports results with tab-separated values (TSV) format. This format is a tabular format that consists of multiple rows with tab-separated elements.

In addition to this TSV format, WISARD provides an option to select the format to be exported, and those options are the followings.

• CSV format --outformat csv

Comma-separated values (CSV) format is similar with TSV, but separates elements by comma(,) character and covers string with double quote(") character. This format is widely used.

• XML format --outformat xml

EXtensible Markup Language (XML) is a markup language that defines a set of rules for encoding documents in a format which is both human-readable and machine-readable (from Wikipedia). WISARD exports the result using this format under --outformat xml, which is compatible with XML 1.0 specification.

NOTE!

NA values will be exported with no value. ex)

• JSON format --outformat json

JSON (JavaScript Object Notation) is an open standard format that uses human-readable text to transmit data objects consisting of attribute–value pairs (from Wikipedia). WISARD exports the result using this format as a single array under --outformat json. In the JSON-style result, each element is an object that contains a record, and each attribute in the object is the columns of the record.

NOTE!

NA values will be exported with no value. ex) 'P_REGR':null

Remove NAs from the output file

If certin information is missing or misspecified, p-values cannot be calculated and NAs are reported. If you want to remove NAs in p-values, --remana can be used. In order to remove those NA p-values from the result of analyses, --remna can be used.

If multiple p-values for a single variant/gene are reported, result for a variant/gene are reported unless all p-values are NA.

Example code

Filter variants of which p-values are in certain range

Results of variants/genes where their p-values are in certain range can be selectively reported by using --pvalrange option. If multiple p-values for a single variant/gene are reported, result for a variant/gene are reported if at least a signe p-value is in the specified range.

Example code

Report computing time for each test

Computational time for most of analysis supported by WISARD can be reported by using --time option.

Example code

Annotation summary [top]

Annotation for association analyses provides various informations about the disease susceptibility locus. WISARD provides some functions for annotation by using information of genetic/physical position for each variant.

Using pre-defined annotation file

An annotation file format of WISARD is exactly equivalent with PLINK. Hence pre-defined annotation files for PLINK are also can be used to WISARD. In order to use those pre-defined annotation file, download it from this link.

Annotate variants with each gene

Result for each variant within a gene can be annotated by using --annogene option and they will be provided in the additional column, ANNO.

Example code

Expading annotation range

WISARD provides further function for annotating variants which are located near genes but not within genes. "--annorange k" makes WISARD annotates all variants of which distances with adjacent gene are less than k basepair.

Analyses supporting annotation functions

For the following analyses with WISARD, functions for annotating each variants can be applied:

• Regression analysis
• Quasi-likelihood-based analysis such as MQLS and FQLS
• MAF estimation
• HWE estimation