newinfile.df: Create empty infile (data frame)

In hmbotelho/htmrenamer: File Renaming Tools for High Throughput Microscopy

Create empty infile (data frame)

Description

Creates an empty microscope infile template, which can be printed to the console and/or saved as a file. The output is structured as a data frame. See the Note section for a description of the infile structure.

Usage

newinfile.df(numrow = 8, numcol = 12, show = FALSE, saveto = character())

Arguments

numrow	integer, the number of rows in the multiwell plate. The default value is 8 (i.e. 96 well plate).
numcol	integer, the number of columns in the multiwell plate. The default value is 12 (i.e. 96 well plate).
show	logical, indicating whether or not to print the result to the console.
saveto	character. If specified, the empty infile template is saved in a file at this location.

Value

Data frame with empty infile template.

Note

The microscope infile is a text file with the following structure:

001--A--01--00--00--data1--data2
002--A--02--01--00--data1--data2
003--A--03--02--00--data1--data2

In the infile, metadata fields are separated by a double dash (--). The meaning of the metadata fields is the following:

• Well number

• Row label (A, B, ...)

• Column label (01, 02, 03, ...)

• Column label (00, 01, 02, ...)

• Row label (00, 01, 02, ...)

• Experimental data 1

• Experimental data 2

Wells are numbered in ascending order, line by line. In the case of a 96 well plate, wells are numbered as shown:

-----1---2---3---4---5---6---7---8---9--10--11--12- --------------------------------------------------- A | 001 002 003 004 005 006 007 008 009 010 011 012 B | 013 014 015 016 017 018 019 020 021 022 023 024 C | 025 026 027 028 029 030 031 032 033 034 035 036 D | 037 038 039 040 041 042 043 044 045 046 047 048 E | 049 050 051 052 053 054 055 056 057 058 059 060 F | 061 062 063 064 065 066 067 068 069 070 071 072 G | 073 074 075 076 077 078 079 080 081 082 083 084 H | 085 086 087 088 089 090 091 092 093 094 095 096

The experimental data fields may contain any relevant information describing the well contents.

See Also

Function newinfile.char creates an empty infile in the form of a character vector.
Function read.infile.df reads infile text files from disk.

Examples

# Infile template for a 96 well plate
newinfile.df()

# Save 384 well plate infile template to the working directory.
# The CSV file extension is recommended.
newinfile.df(numrow = 16, numcol = 24, saveto = "./infile_template.csv")

hmbotelho/htmrenamer documentation built on April 11, 2025, 11:04 p.m.