biomart.SNPid.in.window: Fetches the reference SNP IDs in the spefified window

In alesssia/timesaveR: Widely used function to save time on everyday work

Fetches the reference SNP IDs in the spefified window

Description

Uses biomaRt function to fetch the reference SNP IDs for those SNPs included in the specified window. It uses the given BioMart database.

Usage

biomart.SNPid.in.window(
  chr,
  start,
  end,
  mart,
  with.position = FALSE,
  with.alleles = FALSE
)

Arguments

chr	chromosome number (1, 2, ...)
start	fist position of the window (included)
end	last position of the window (included)
mart	BioMart database
with.position	whether including chromosome name and start and end position (default: false)
with.alleles	whether including variant alleles (default: false, if with.position==TRUE is forced to TRUE)

Value

reference SNP IDs, or reference SNP IDs plus genomic coordinates and alleles

Author(s)

Alessia Visconti

Examples

mybiomart <- biomart.fetch.SNP.grch37.mart()
biomart.SNPid.in.window(1, 1, 10100, mybiomart)
biomart.SNPid.in.window(1, 1, 10100, mybiomart, with.position=TRUE)
biomart.SNPid.in.window(1, 1, 10100, mybiomart, with.alleles=TRUE)

alesssia/timesaveR documentation built on Jan. 26, 2024, 5:21 p.m.