rod.read: Reading of ROD raw timecourse data. Deprecated.

In qfa: Tools for Quantitative Fitness Analysis (QFA) of Arrayed Microbial Cultures Growing on Solid Agar Surfaces

Description

Reads in and binds together all of the ROD output files in a directory, so they are checked and ready for bayesian or likelihood inference . Deprecated.

Usage

rod.read(path=".",files=c(),inoctimes="BarcodeTimes.txt",background="",
treatments=c(),barcodes=c(),master.plates=c(),screen.names=c(),ORF2gene = "")

Arguments

path	The path to the folder containing the ROD files to be read: working directory by default. Do not have other text files here.
files	Character vector giving locations of ROD files to be read - overrides path
inoctimes	A text file whose first column includes the barcodes in the ROD files and whose second column is the corresponding inoculation date.times. Taken relative to path if specified.
background	The genetic background of the colonies in the ROD files
treatments	Store data only for the plates with treatments in this character vecor; all by default.
barcodes	Store data only for the plates with barcodes in this character vecor; all by default.
master.plates	Store data only for the plates from master.plates in this character vecor; all by default.
screen.names	Store data only for the plates with screen.names in this character vecor; all by default.
ORF2gene	Path to a tab-delimited text file containing two columns (with no headers) associating unique, systematic strain identifiers (e.g. yeast ORF Y-numbers) with human readable gene names (e.g. standard names from SGD).

Value

An R data.frame where each row corresponds to a single observation on a single colony, with the value of the growth measurement in 'Growth', and the date and time of the measurement in 'Date.Time'. Other information about the observation is stored in the other columns.

qfa documentation built on Feb. 22, 2020, 3:01 a.m.