ZC_nH2O {canprot}R Documentation

Calculate Compositional Differences

Description

Compare elemental abundances per residue and compositional oxidation and hydration state between groups of proteins.

Usage

  ZC_nH2O(pdat, plot.it = TRUE)
  CNS(pdat)

Arguments

pdat

list, data object generated by get_pdat

plot.it

logical, make a scatterplot?

Details

ZC_nH2O can be used to summarize differences in the average oxidation state of carbon (ZC) and water demand per residue (n̄H2O) between groups of down- and up-expressed proteins. The expression pattern is taken from the value of up2 returned by one of the pdat_ functions: down (up2==FALSE) or up (up2==TRUE). The function prints the difference of means, common language effect size (CLES, in percent), and p-value.

If plot.it is TRUE, a scatterplot is also produced.

Similarly, CNS calculates mean differences, CLES, and p-value for elemental abundance per residue: Carbon, Nitrogen, and Oxygen.

Value

For ZC_nH2O, a data frame is returned invisibly containing the columns dataset, description, n1, n2, ZC.mean1, ZC.mean2, ZC.diff, ZC.CLES, ZC.p.value, nH2O.mean1, nH2O.mean2, nH2O.diff, nH2O.CLES, and nH2O.p.value. In CNS, columns with mean1, mean2, diff, CLES, and p.value are present for each of C, N, and S.

Examples

data(canprot)
pd <- get_pdat("JKMF10")
ZC_nH2O(pd)
CNS(pd)

[Package canprot version 0.1.0 Index]