bbgp_snpData: Obtaining counts data in the format of example snpData by...

In GPrank: Gaussian Process Ranking of Multiple Time Series

Description

Function for extracting the required data for the experimental evolution application.

Usage

bbgp_snpData(dataFileName, noHeaderLines = 1, noInfoColumns = 3,
  noOptions = 6, sep = ":")

Arguments

dataFileName	Name of the raw data file
noHeaderLines	Number of header lines, set to 1 by default.
noInfoColumns	Number of columns which contain information about the SNP locations. These columns are used to construct SNP IDs.
noOptions	Number of possible alterations separated by the character defined in "sep" Default is 6, assuming the form A:T:C:G:N:Del
sep	Character which separates the alterations. Default is set to ":".

Value

List of snpData which contains counts in the "counts" matrix and sequencing depth values in the "seq_depth" matrix. SNP IDs are stored as row names, and time points are stored as column names.

Author(s)

Hande Topa, [e-mail]

Examples

# dataFileName="sampleCountsData"
# snpData=bbgp_snpData(dataFileName)

GPrank documentation built on May 2, 2019, 3:35 p.m.