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The IgAScores package is used to calculate taxon-level IgA binding scores from IgA-Seq data. It also includes several helper functions for managing microbiome data and simulating IgA-Seq datasets for method testing.
For a detailed consideration of the methods that are used for scoring IgA-Seq data, see the associated paper.
This package can be installed from GitHub using devtools.
if (!require(devtools)){install.packages('devtools')}
install_github("microbialman/IgAScores", build_vignettes = TRUE)A detailed overview of how to run the various functions within
IgAScores can be found in the R vignette:
vignette("IgAScores")
A brief summary of the main igascores() function is given below:
#load in IgAScores
library(IgAScores)
#dataframes with counts for the bacterial taxa in the IgA+ and IgA- fractions, as would be produced by 16S rRNA appraoches such as DADA2
igapos <- data.frame(Sample1=c(100,0,1,2,10),Sample2=c(110,0,11,42,50),Sample3=c(140,60,10,3,0))
iganeg <- data.frame(Sample1=c(200,0,40,20,4),Sample2=c(10,30,110,2,5),Sample3=c(30,20,0,123,20))
taxnames <- c("Taxon1","Taxon2","Taxon3","Taxon4","Taxon5")
rownames(igapos) <- taxnames
rownames(iganeg) <- taxnames
#convert the counts to relative abundances using the included helper function
igapos <- relabund(igapos)
iganeg <- relabund(iganeg)
#iga+ and iga- fraction sizes per sample (fraction, if a percentage divide by 100)
possize <- c(Sample1=0.04,Sample2=0.05,Sample3=0.03)
negsize <- c(Sample1=0.54,Sample2=0.47,Sample3=0.33)
#set a pseudo count for handling zero values in some scoring methods
#this should be of a similar value of the minimum non-zero observed value (e.g. if minum values is 0.007 use 0.001)
pseudo <- 0.001
#default method is the probability ratio "probratio"", additional methods available are "prob"", "kau"" and "palm".
prscores <- igascores(posabunds = igapos, negabunds = iganeg,
possizes = possize, negsizes = negsize,
pseudo = pseudo)
print(prscores)These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.