RSAfromAcup: Convert Acup to RSA

In mooredf22/protlocassign: Estimation of protein distribution from quantitative subcellular fractionation experiments using a constrained proportional assignment model

Convert Acup to RSA

Description

Convert Acup (relative amount) profiles to RSA (relative specific amount) profiles

Usage

RSAfromAcup(Acup, NstartMaterialFractions, totProt = NULL)

Arguments

Acup	data frame of specified protein (row name) Acup profiles; amount of given protein in fraction / amount of that given protein in starting material (see help file for protAcup_test).
NstartMaterialFractions	Number of fractions that reconstitute the starting material, e.g., a complete set of differential centrifugation fractions. For experiment AT5, it is 6 ( N, M, L1, L2, P, and S).
totProt	vector of total protein amounts (derived from a given amount of starting material) in each of the fractions comprising the profile

Value

RSA profiles. RSA is the ratio of two ratios: the numerator is the amount of a given protein in a particular fraction divided by the amount of that given protein in the starting material while the denominator is amount of total protein in a particular fraction divided by the amount of total protein in the starting material. The RSA describes the fold-enrichment (RSA>1) or depletion (RSA<1) of a protein during the fractionation process, and is analogous to the relative specific activity term used in classical analytical subcellular fractionation

Examples

data(protAcup_test)
data(totProtAT5)
protRSA_out1 <- RSAfromAcup(protAcup_test[,seq_len(9)], 
     NstartMaterialFractions = 6,
     totProt=totProtAT5)
round(head(protRSA_out1), digits=4)
str(protRSA_out1)

mooredf22/protlocassign documentation built on Sept. 13, 2023, 3:57 p.m.