I have a data frame consisting of 1893 p-values that I convert to qvalues using the R package qvalue:
pvals <- read.table("p_values.csv",header=T,sep=",",dec=".")
The qvalue manual states you can directly plot (using the qplot function) the output of the qvalue function by:
qobj <- qvalue(pvals)
qplot(qobj)
However this results instead in an error:
Don't know how to automatically pick scale for object of type qvalue. Defaulting to continuous Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class ""qvalue"" to a data.frame
Anyone have an idea how to fix this and make qplot plot the output of the qvalue function?