DataAnalysis: Main function call to generate microbial density data from...

In econtijoch/Biomass-Workflow: Microbial Density Data Generation and Analysis Tools

Description

Main function call to generate microbial density data from DNA extraction protocol

Usage

DataAnalysis(plate_reader_file, mapping_csv_file, exp_id = "EXP_ID",
  standards_plate_reader_file = plate_reader_file,
  standards_mapping_csv_file = mapping_csv_file, volume = 2, scale = 3.5,
  shiny = FALSE, type_plate = NULL, type_standards_plate = NULL,
  print = FALSE, ...)

Arguments

plate_reader_file	raw file from plate-reader (can be in .xls format, or .csv), but will only read in first sheet of excel file
mapping_csv_file	a .csv file that contains information as to the location of the samples, the sample types, and their mass. A sample file has been included in this package and can be found at https://github.com/econtijoch/Biomass-Workflow/blob/master/SampleMapping.csv
exp_id	a string that indicates the name of the experiment (used to label the plot of your standard curve)
standards_plate_reader_file	OPTIONAL: if your standards are not on the same plate as your samples, you will need to provide the file path of the plate reader file for the standards (Default is to use same plate as samples)
standards_mapping_csv_file	OPTIONAL: if your standards are not on the same plate as your samples, you will also need to provide the file path of a mapping file for the standards plate (Default is to use same plate as samples)
volume	OPTIONAL: The volume (in uL) used to quantify DNA with Qubit (Default = 2)
scale	OPTIONAL: The scale factor used in the DNA isolation protocol (Defualt = 3.5, which corresponds to taking 200uL of supernatant from the 700uL of the DIB added). For phenol extraction, use scale = 1.
shiny	OPTIONAL: necessary for running with shiny app interface since filenames are not the same.
type_plate	OPTIONAL: necessary for running with shiny app, must specify file type of plate
type_standards_plate	OPTIONAL: necessary for running with shiny app, must specify type of plate for standards
print	OPTIONAL: whether or not to save a copy of the standards curve to the working directory
...	Optional arguments to pass

Value

output table with DNA concentrations, microbial density, metadata, and useful computations for downstream (sequencing) applications, and a plot of the standard curve

econtijoch/Biomass-Workflow documentation built on May 15, 2019, 7:59 p.m.