GPrank (version 0.1.4)

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

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.

Examples

# NOT RUN {
# dataFileName="sampleCountsData"
# snpData=bbgp_snpData(dataFileName)

# }