calculateLDSingle: Calculate pairwise LD for a target SNV to its neighbourhood

In mklarqvist/rtomahawk: Tools for computing, querying and storing linkage-disequilibrium data

Description

Some additional details about this S4 generic and its methods. The extra blank line between this section and the title is critical for roxygen2 to differentiate the title from the description section.

Usage

calculateLDSingle(x = "twk", interval = "ANY", window = "numeric",
  minP = "numeric", minR2 = "numeric", threads = "numeric",
  verbose = "logical", progress = "logical", ...)

Arguments

x	Integer representing the sorted state of the file.
interval	This parameter can be either a character string encoded as "CHR:POS" or a GenomicRanges object overlapping a single position.
window	Neighbourhood in base-pairs.
minP	Largest P-value to report.
minR2	Smallest R-squared (R2) value to report.
threads	Number of Tomahawk threads used to unpack and compute the association data.
verbose	Flag triggering verbose output (written to std::cerr). This will usually, but not always, be appropriately handled by R.
progress	This flag will trigger a detached thread internal to Tomahawk that will tick progression every 30 seconds to the console. Note that R NEVER cleans up this thread and it will tick until the R instance is closed.

Value

Returns a twk object with the loaded data.

Author(s)

Marcus D. R. Klarqvist <[e-mail]> | <https://mdrk.me>

See Also

twk_data, twk_header, twk_filter, and twk

Examples

# This example assumes you have a Tomahawk file called "1kgp3_chr6.twk" in
# your current working directory.
twk2<-new("twk")
[e-mail] <- "1kgp3_chr6.twk"
y<-calculateLDSingle(twk2, "6:20682622", threads = 4, window = 100000)
# Example using GenomicRanges class.
require(GenomicRanges)
g <- GRanges("6", IRanges(20682622, 20682622))
y<-calculateLDSingle(twk2, g, threads = 4, window = 100000)

mklarqvist/rtomahawk documentation built on May 16, 2019, 5:01 a.m.