Fluidigm (version 0.2)

similarityMatrix: Calculate the similarity matrix

Description

Performs pairwise similarity analysis on genotypic data.

Usage

similarityMatrix(
  file = NA,
  mibs.file = NA,
  pairs.file = NA,
  ped.file = NA,
  group = NA,
  plots = TRUE,
  similarity = 0.85,
  verbose = TRUE,
  verbosity = 1
)

Value

Does not return a value. Creates output files in the same directory as the input files.

Arguments

file

Input file path. Default: NA.

mibs.file

MIBS input file path. Default: NA.

pairs.file

PAIRS input file path. Default: NA.

ped.file

PED input file path. Default: NA.

group

Sample identifier for statistics. Default: NA.

plots

Should plots be created? Default: TRUE.

similarity

Similarity threshold. Default: 0.85.

verbose

Should output be verbose? Default: TRUE.

verbosity

Verbosity level. Default: 1.

Details

Reads genotype data, performs pairwise similarity calculations, generates plots, and outputs data for further analysis.

Examples

if (FALSE) {
     similarityMatrix(file = file.path(outdir, "example_data.csv.GOOD"))
}