Usage
"transform"(`_data`, ...)
t_ColCenter(x, ...)
t_ColScale(x, ...)
t_Log(x, ...)
t_NA2Zero(x, ...)
t_Threshold(x, entry.min=2, row.min=2, col.min=2)
Examples
#### simple log-transform
transform (xx1, t_Log)
#### additional filters
transform (xx1, t_NA2Zero, t_Threshold, t_Log)
#### what is lost with more stringent filtering of low-abundance annotations
yy <- transform (xx2, t_NA2Zero, t_Threshold, t_Log)
zz <- transform (xx2, t_NA2Zero, t_Threshold=list(entry.min=5, row.min=10), t_Log)
setdiff (rownames (yy), rownames (zz))
#### each sample centered around zero; scaling columnwise by standard deviation
transform (xx4, t_NA2Zero, t_Threshold, t_Log, t_ColCenter, t_ColScale)
#### defining a new transformation that indicates presence / absence
t_Indicator <- function (x, ...) { ifelse (x,1,0) }
transform (xx1, t_Threshold = list(entry.min=5), t_Indicator)