genesbylocation: Find genes that are located in a specified genomic region.

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

Description

Find genes within a given genomic region.<br> Either select an organism and a genomic sequence from the pull-down menu or enter a genomic sequence ID from any EuPathDB species (e.g. "AAEL01000057", "Pf3D7_04", "TGME49_chrIa", "ctg02_305", "DS170425").

The Start and End locations correspond to the coordinates of the gene(s) on the chromosome.

Arguments

organism	Organism
chromosomeOptional	Select chromosome for a selected organism or enter genomic sequence ID. If you provide both you will get both.
sequenceId	Enter an identifier for a genomic sequence. The IDs correspond to the accession numbers in the GenBank records supplied by the sequencing centers. Wild cards are permitted in most queries, i.e. use AAEE* to ask for all <i> C.parvum </i> contigs. Genes By Chromosomal Location does not allow wildcards.
start_point	Select the distance (in nucleotides) to the start
end_point	Select the nucleotide you would like to end in. Note that 0 equals the end so you can get genes right up to the end of the sequence. The default settings start = 1 and end = 0 will give you results from the entire sequence.
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

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