index: Indexing function
In ctsGE: Clustering of Time Series Gene Expression data

Description Usage Arguments Details Value See Also Examples

View source: R/PreparingTheIndexes.R

Takes a numeric vector and return an expression index (i.e., a sequence of 1,-1, and 0)

1	index(x, cutoff)

`x`	A numeric
`cutoff`	A numeric, dermine the threshold for indexing

The function defines limits around the center (median or mean), +/- cutoff value in median absolute deviation (MAD) or standard deviation (SD) units respectively.The user defines a parameter cutoff that determines the limits around the gene-expression center. Then the function calculates the index value at each time point according to:

0: standardized value is within the limits (+/- cutoff)
1: standardized value exceeds the upper limit (+ cutoff)
-1: standardized value exceeds the lower limit (- cutoff)

Gene expression index

PreparingTheIndexes

rawCounts <-
c(103.5, 75.1, 97.3, 27.12, 34.83, 35.53, 40.59, 30.84, 16.39, 29.29)

(sCounts <- scale(rawCounts)[,1])# standardized mean-base scaling

cutoff <- seq(0.2,2,0.1)    # different cutoff produce different indexes

for(i in cutoff){print(index(sCounts,i))}