CallDosage: Calls dosage for a given input file

In dsherma7/PolyploidDosageCalling: Calls the Dosage From Tetraploid qPCR Data (CT/RQ Values)

Description

Uses multiple models to fit the data, then uses each of these models to determine both the best fit, and liklihood of that fit.

Usage

CallDosage(File, Control.File = "Controls.csv", Output.Dir = "Output",
  Directory = NULL, sheet = "Results", Console = F,
  Target.Column = "Target.Name", RQ.Threshold = 7,
  Output.File = "Dosage.csv", REF.Vars = c("CT"))

Arguments

File	Name of the file containing the raw data from a Quant Studio qPCR run. The column Clone-plant_ID must be added.
Control.File	Name of the file containing the controls. Must contain 2 columns, Name and Dosage, with Name matching the values in Clone-Plant_ID for control samples. (Default = Controls.csv)
Directory	The directory containing the necessary files. Default to NULL which will use current directory.
sheet	The name in File where Clone-Plant_ID and RQ values are stored. Default = "Results".
Console	Should plots be printed to the console? Default is False which prints the plots to Output.Dir.
Target.Column	Column containing the Target Assays. Default="Target.Name"
RQ.Threshold	If RQ goes above this value we know something went wrong with the data. (Default = 7), since RQ should never be above 5.
Output.File	The name of the output file containing the final dosage calls. Defaults to Dosage.csv.
REF.Vars	REF.vars will be included in the output file with the reference assay values. (Default = CT)

Value

A dataset containing the dosage calls of each of the methods and a final determination of the dosage and likelihood.

See Also

?CallPA for calling the presence/absence of provided data

Examples

# Obtain the appropriate Control and Raw Data files. You can find these in the 
# data-raw/ folder of the Quadrophenia package files.They should match the data below.

# A 41 line header
# Followed by the output of QuantStudio's Results sheet
# Note that Clone-plant_ID must be added manually to this file

require(Quadrophenia)
RawData.Assay1CN[1:41,1] # Header
RawData.Assay1CN[42,]    # Columns of data

# The controls file has two columns: Name and Dosage. Name must 
# match the Clone-plant_ID column for the controls in the raw data file.

head(ControlsAssay1CN)

# Then run CallDosage() with these files as inputs

output = CallDosage(File='RawData.Assay1CN.xls',Control.File='ControlsAssay1CN.csv')

# The output directory Output/ should contain 1 .csv file and a Plots/ directory.
# The Plots/ directory contains two plots, one standard for manual calling, and 1
# plot showing the distribution of each class. The output file has columns for the
# Dosage calls as well as a likelihood for each call.

head(output)

## Other ways to run CallDosage()
# You could also specifiy an output file or a directory to look for the raw data files

dir.create('Files/')
file.copy(c('RawData.Assay1CN.xls','ControlsAssay1CN.csv'),'Files/')
output = CallDosage(File='RawData.Assay1CN.xls',
                    Control.File='ControlsAssay1CN.csv',
                    Directory='Files/',Output.Dir='NewOutput')

# Or specify the files in Files/ wihout specifying the directory. You can
# also change the name of the output file to something more informative.

output = CallDosage(File='Files/RawData.Assay1CN.xls',
                    Control.File='Files/ControlsAssay1CN.csv',
                    Output.Dir='ThirdOutput',
                    Output.File='ThirdOutputDosage.csv')

# Duplicates will automatically be renamed to avoid conflicts

output = CallDosage(File='Files/RawData.Assay1CN.xls',
                    Control.File='Files/ControlsAssay1CN.csv',
                    Output.Dir='ThirdOutput',
                    Output.File='ThirdOutputDosage.csv')

# Clean up the test files
unlink(c('Files','Output','ThirdOutput'),recursive=T)

dsherma7/PolyploidDosageCalling documentation built on May 23, 2019, 6:06 p.m.