R: Run the Fluidigm Analysis Script Together

fluidigmAnalysisWrapper {Fluidigm}

R Documentation

Run the Fluidigm Analysis Script Together

Description

This function serves as a wrapper for the entire analysis pipeline. It takes a Fluidigm input file and performs several operations including conversion to 'PLINK' format, error estimation, calculation of pairwise similarities, determination of pairwise similarity loci, and calculation of the similarity matrix.

Usage

fluidigmAnalysisWrapper(
  file,
  out = NA,
  outdir = NA,
  db = NA,
  appendSamplesToDB = FALSE,
  map = NA,
  keep.rep = 1,
  neg_controls = NA,
  y.marker = NA,
  x.marker = NA,
  sp.marker = NA,
  plots = TRUE,
  allele_error = 5,
  marker_dropout = 15,
  no_marker = 50,
  male.y = 3,
  male.hetX = 0,
  female.y = 0,
  female.Xtot = 8,
  female.hetXtot = 3,
  warning.noYtot = 2,
  warning.noHetXtot = 3,
  rearrange = TRUE,
  group = NA,
  fixNames = TRUE,
  sexing = TRUE,
  similarity = 0.85,
  verbose = TRUE,
  verbosity = 1,
  missing.geno = "0 0",
  overwrite = FALSE
)

Arguments

`file`	A string specifying the path to the Fluidigm input file.
`out`	A string specifying the output file name. If left empty, the original basename of the input file will be used.
`outdir`	A string specifying the output folder. If left empty the original folder path of the input file will be used.
`db`	A string specifying the filepath to the database file. If not provided, the function will proceed with the existing data.
`appendSamplesToDB`	A logical indicating whether new samples should be added to the database. Default is FALSE.
`map`	A string specifying the filepath to the PlateDnoY.map file. If not provided, the function will use the map file with the same name as the ped file.
`keep.rep`	A numeric value indicating the number of replicates to keep. Default is 1.
`neg_controls`	A vector specifying the names of negative controls. Default is NA.
`y.marker`	A vector specifying the Y markers for sexing. Default is NA.
`x.marker`	A vector specifying the X markers for sexing. Default is NA.
`sp.marker`	A vector specifying the markers used for species identification. Default is NA.
`plots`	A logical indicating whether plots should be created. Default is TRUE.
`allele_error`	A numeric value specifying the threshold for RERUN on Allele errors. Default is 5.
`marker_dropout`	A numeric value specifying the threshold for RERUN on Marker dropout. Default is 15.
`no_marker`	A numeric value specifying the number of markers. Default is 50.
`male.y`	A numeric value specifying the threshold for sexing, male y-chromosome markers. Default is 3.
`male.hetX`	A numeric value specifying the threshold for sexing, heterozygote x-chr markers. Default is 0.
`female.y`	A numeric value specifying the threshold for sexing, female y-chromosome markers. Default is 0.
`female.Xtot`	A numeric value specifying the threshold for sexing, total female x-chr markers. Default is 8.
`female.hetXtot`	A numeric value specifying the threshold for sexing, heterozygote x-chr markers. Default is 3.
`warning.noYtot`	A numeric value specifying the threshold for sexing, when should warning be triggered. Default is 2.
`warning.noHetXtot`	A numeric value specifying the threshold for sexing, when should warning be triggered. Default is 3.
`rearrange`	A logical indicating whether the ped/map output should be rearranged in order of provided map file. Default is TRUE.
`group`	A string specifying the sample identifier for statistics. Default is NA.
`fixNames`	A logical indicating whether whitespaces from sample names should be automatically removed. Default is TRUE.
`sexing`	A logical indicating whether sexing should be performed. Default is FALSE.
`similarity`	Similarity threshold. Default: 0.85.
`verbose`	A logical or numerical value indicating whether the output should be verbose. Default is TRUE.
`verbosity`	A numerical value indicating the level of verbosity. Set to a higher number for more details. Default is 1.
`missing.geno`	A character string specifying how missing values should be coded. Default is "0 0".
`overwrite`	A logical indicating wheter the original map file should be overwritten or not. Default FALSE

Details

The function first checks the input parameters and sets default values if necessary. It then runs the following functions in order:

fluidigm2PLINK: Converts the Fluidigm data to PLINK format.
estimateErrors: Estimates errors in the PLINK ped files.
calculatePairwiseSimilarities: Calculates pairwise similarities between genotypes.
getPairwiseSimilarityLoci: Determines the loci of pairwise similarities.
similarityMatrix: Calculates the similarity matrix. The function prints a completion message when all operations are done.

Value

A list containing the following elements: gensim, a matrix indicating if genotypes are called correctly for replicates and/or if genotypes are missing summs, a matrix with summary statistics

References

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.
Purcell, Shaun. PLINK. https://zzz.bwh.harvard.edu/plink/

Examples

## Not run: 
  fluidigmAnalysisWrapper(file="path/to/your/file.csv", map="path/to/your/mapfile.map")

## End(Not run)

[Package Fluidigm version 0.2 Index]