similarityMatrix {Fluidigm} | R Documentation |
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
)
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.
Value
Does not return a value. Creates output files in the same directory as the input files.
Examples
## Not run:
similarityMatrix(file = file.path(outdir, "example_data.csv.GOOD"))
## End(Not run)
[Package Fluidigm version 0.2 Index]