makeBinarySig: Convert p-values to binary significance calls
In jtlovell/RNAseqDE: A pipeline for differential expression analyses in R

Description Usage Arguments Details Value Examples

makeBinarySig Convert some sort of significance distribution to binary signifcance calls.

1 2	makeBinarySig(x, alpha = 0.05, what = "q.value", na.include = TRUE, verbose = TRUE)

`x`	A dataframe or matrix containing the significance (p/q/fdr p) values to convert
`alpha`	The threshold that defines what is and is not significance
`what`	Character vector defining a string to look for in the column names. For example, "q.value"
`na.include`	Logical, should NAs be classified as not significant? If false, all rows with any NAs are dropped.
`verbose`	Logical, should the number of significant values be printed

Given a matrix with p/q values, this function greps for the string in "what" and classifies each column as either significant (1) or not (0). Esspecially useful for a dataset that has many p-value or q-value columns

a dataframe with all values in the original matrix with column names containing what, where the values have been transformed to binary

## Not run: 
data(kidney) # from SimSeq
counts<-kidney$counts
counts<-counts[sample(1:nrow(counts),1000),]
info<-data.frame(rep=kidney$replic, treatment=kidney$treatment)
stats<-pipeLIMMA(counts=counts, info=info, formula = " ~ treatment", block=NULL)
sig<-makeBinarySig(x= stats$stats, what="Pvalue")

## End(Not run)