canprot (version 0.1.2)

get_comptab: Calculate Compositional Differences

Description

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

Usage

get_comptab(pdat, var1="ZC", var2="nH2O", plot.it = FALSE, mfun = "median")

Arguments

pdat

list, data object generated by get_pdat

var1

character, the first variable

var2

character, the second variable

plot.it

logical, make a scatterplot?

mfun

character, specifying use of the median or mean function

Value

A data frame is returned invisibly containing the columns dataset, description, n1, n2, and two sets of columns (var.mfun1, var.mfun2, var.diff, var.CLES, var.p.value), where var is replaced by the values of var1 and var2, respectively, and mfun is replaced by the value of mfun.

Details

get_comptab can be used to summarize differences of compositional variables between down (group 1)- and up (group 2)-expressed proteins. The available compositional variables are:

ZC	average oxidation state of carbon (; see ZC)
nH2O	water demand per residue ()
nC	number of carbon atoms per residue
nN	number of nitrogen atoms per residue
nS	number of sulfur atoms per residue
V0	standard molal volume per residue
nAA	protein length (number of amino acids)

Volume is calculated using amino acid group additivity as described by Dick et al. (2006).

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 medians (or means), common language effect size (CLES, in percent), and p-value.

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

References

Dick, J. M., LaRowe, D. E. and Helgeson, H. C. (2006) Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. Biogeosciences 3, 311--336. https://doi.org/10.5194/bg-3-311-2006

Examples

# NOT RUN {
library(CHNOSZ)
pd <- get_pdat("JKMF10")
# default variables: ZC and nH2O
get_comptab(pd, plot.it = TRUE)
# protein length and per-residue volume
get_comptab(pd, "nAA", "V0", plot.it = TRUE)
# }