Parse the annotations for one single ELISA plate from a section of a file and output the annotations for standard and unknown separately.
characters to specify the path and name of the annotation file
data.frame containing standard concentration data. Only first two columns are used with first one to be the standard IDs and second the concentrations.
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
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.
a list of data.frames holding the annotations for the plate.
1 2 3 4 5 6 7 8
#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.
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