fetch.intensities: Retrieve genotype calls and hybridization intensities

In andrewparkermorgan/genodb: R Access to Genotype Databases

Description

Retrieve genotype calls and hybridization intensities

Usage

fetch.intensities(ids, markers = NULL, chr = NULL, start = NULL,
  end = NULL, raw = FALSE, by = c("id", "name"), db = c("mm", "muga",
  "mda", "giga"), verbose = FALSE)

Arguments

ids	vector of sample IDs (names or internal database IDs)
markers	character vector of marker names for which calls and intensities will be returned
chr	limit to markers on these chromosome(s)
start	limit to markers with genomic position >= start (requires chr)
end	limit to markers with genomic position <= end (requires chr)
raw	logical; if TRUE, return raw rather than Illumina-normalized intensities
by	search for samples by unique numeric ID ("id") or by human-readable sample name ("name")
db	which database to search: must be one of "mm" (MegaMUGA), "muga", (MUGA) or "giga" (GigaMUGA)
verbose	logical; if TRUE, show progress meter and diagnostic messages to console

Details

Most of our databases are indexed by sample, chromosome, and position but not by marker name: retrieving data for specific markers (as opposed to genomic regions) may be very slow. It is *always* advisable to use numeric sample IDs (guaranteed unique within a database) rather than human-readable names (which may be duplicated).

Value

a data.table with one row per sample-marker combination

andrewparkermorgan/genodb documentation built on May 10, 2019, 11:09 a.m.