index: Indexing function

Description Usage Arguments Details Value See Also Examples

View source: R/PreparingTheIndexes.R

Description

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

Usage

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index(x, cutoff)

Arguments

x

A numeric

cutoff

A numeric, dermine the threshold for indexing

Details

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:

  1. 0: standardized value is within the limits (+/- cutoff)

  2. 1: standardized value exceeds the upper limit (+ cutoff)

  3. -1: standardized value exceeds the lower limit (- cutoff)

Value

Gene expression index

See Also

PreparingTheIndexes

Examples

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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))}

ctsGE documentation built on Nov. 8, 2020, 11:06 p.m.