read.annotation {ELISAtools}

Read the annotation of single ELISA plate

Description

Parse the annotations for one single ELISA plate from a section of a file and output the annotations for standard and unknown separately.

Usage

read.annotation(annotation, std.conc)

Arguments

annotation

characters to specify the path and name of the annotation file

std.conc

data.frame containing standard concentration data. Only first two columns are used with first one to be the standard IDs and second the concentrations.

Details

The annotation file may contain annotations for more than one plate. Each plate is marked by "Plate: plate 1..." and "~End". This function is fed in with the content for each section and we do actually parsing in here. Store the annotations into data frame. It also parse the standard concentration and include this information in the data frame. For each section,we expect the following format

	1	2	3	4	...
C	s1	s1	sample1	sample1	...
D	s2	s2	sample2	sample	...
...	...	...	...	...	...

In addition, the row name and column names indicate the the plate row and column indices. As input, the stardard and unknown are returned separately in two tables.

Value

a list of data.frames holding the annotations for the plate.

Examples

#get example annotation file path from the system folder
fileName<-system.file("extdata", "annote_single.txt", package="ELISAtools")
#prepare the standard concentration file.
std.conc<-data.frame(id=c("s1","s2","s3","s4","s5","s6"), conc=c(1:6))
#read the data as a data frame.
ann<-read.table(fileName, header=TRUE,  sep="\t", stringsAsFactors=FALSE)

#call to do the reading.