snpsbyisolatepattern: Find SNPs that distinguish two sets of isolates.

In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description

Find SNPs that distinguish two sets of isolates. Note that you can determine the specificity of the SNPs. For the most specific SNPs, you should make the number of isolates equal to the number of identifiers you are querying for in each set. The default ids for Set A are the result of a query for isolates from Malawi (8 isolates) and Set B are the result of a query for isolates from Brazil (12 isolates).

Arguments

organism	Organism Provide one or more values. Use comma as a delimter.
signature	Used to pass the Users Signature to the component sites
isolate_set_a	input a comma delimited set of isolate ids, or upload a file.
set_a_percent	Lower Bound on the percentage of isolates in set A that have the same allele at any SNP position. Note: for the highest confidence SNPs, this percentage should be 100.
isolate_set_b	input a comma delimited set of isolate ids, or upload a file.
set_b_percent	Lower Bound on the percentage of isolates in set B that have the same allele at any SNP position. Note: for the highest confidence SNPs, this percentage should be 100.
o-fields	Single valued attributes of the feature. Provide one or more values. Use comma as a delimter.
o-tables	Multi-valued attributes of the feature. Provide one or more values. Use comma as a delimter.
.convert	a logical value or a function that controls how the result of the method is returned. If this is a function, the character string or raw vector is passed to this function and it converts it appropriately. If this is a logical value and TRUE, then we attempt to convert the result based on its Content-Type returned by the Web server. If this is FALSE, the value from the Web server is returned as is.
.url	the URL for the Web request. This defaults to the correct value, but can be specified by the caller if the method is available at a different URL, e.g. locally or in a mirror server.
.json	a logical value controlling whether to use the JSON or the XML version of the method

Value

text/xml text/plain

duncantl/REuPathDB documentation built on May 15, 2019, 5:28 p.m.