genesbysnps: Find genes which have SNPs meeting specific criteria...

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

Description

Search for genes by SNP density, the number of SNPs of different classes, ratio of non-synonymous to synonymous, etc. Note that if you don't care about one of the parameters, don't change the defaults on that parameter and you will get all genes that contain SNPs between the reference and comparator strains irrespective of that parameter.

Arguments

organism	Organism Provide one or more values. Use comma as a delimter.
snp_strain_a	Choose a reference from the list of strains. Strains are sorted by number of SNPs in descending order.
snp_strain_m	Choose a comparator(s) from the list to compare to your reference. Strains are ordered by number of SNPs in descending order.
snp_stat	Choose the class of SNP you want to query on ... choose minumum and maximum numbers below
occurrences_lower	Lower Bound on the number of SNPs of the selected class
occurrences_upper	Upper Bound on the number of SNPs of the selected class. NOTE: Leaving this parameter value empty means you don't care what the upper bound is.
dn_ds_ratio_lower	Lower Bound on the ratio of non-synonymous to synonymous coding snps
dn_ds_ratio_upper	Upper Bound on the ratio of non-synonymous to synonymous coding snps. NOTE: Leaving this parameter value empty means you don't care what the upper bound is.
snp_density_lower	Find genes containing a density of coding snps greater than this parameter. Density is expressed in number of snps / KB of coding sequence
snp_density_upper	Find genes containing a density of coding snps less than this parameter. Density is expressed in number of snps / KB of coding sequence. NOTE: Leaving this parameter value empty means you don't care what the upper bound is.
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.