calculate_PPIscore: Calculate Pairwise Protein Profile Similarity using Different...

In MACP: Macromolecular Assemblies from Co-Elution Profile (MACP)

Calculate Pairwise Protein Profile Similarity using Different Metrics

Description

This function first removes proteins pairs for which two proteins never occurred in the same fractions, then computes pairwise protein similarity using up to 18 metrics (by default all the 18 measures are activated). This function also provides users with an option to choose an appropriate co-fractionation correlation score cut-off using the 'corr_cutoff' argument, if argument 'corr_removal' is set to TRUE.

Usage

calculate_PPIscore(
  x,
  pcc = TRUE,
  PCCN = TRUE,
  pcc_p = TRUE,
  spearman = TRUE,
  kendall = TRUE,
  bicor = TRUE,
  weighted_rank = TRUE,
  cosine = TRUE,
  jaccard = TRUE,
  dice = TRUE,
  apex = TRUE,
  minfo = TRUE,
  bayesian = TRUE,
  wcc = TRUE,
  euclidean = TRUE,
  manhattan = TRUE,
  canberra = TRUE,
  avg.distance = TRUE,
  rept = 10,
  corr_removal = FALSE,
  corr_cutoff = 0.5
)

Arguments

x	A co-elution data matrix with proteins in rows and fractions in columns.
pcc	If TRUE, computes pairwise protein profile similarity using Pearson correlation metric.
PCCN	If TRUE, computes pairwise protein profile similarity using Pearson correlation plus noise.This function is adapted from the PCCN function in the SMED package.
pcc_p	If TRUE, computes P-value of the Pearson correlation.
spearman	if TRUE, computes pairwise protein profile similarity using spearman correlation.
kendall	if TRUE, computes pairwise protein profile similarity using kendall correlation.
bicor	if TRUE, computes pairwise protein profile similarity using biweight midcorrealtion (bicor) correlation.
weighted_rank	if TRUE, computes pairwise protein profile similarity using weighted rank measure.
cosine	If TRUE, computes pairwise protein profile similarity using cosine metric.
jaccard	If TRUE, computes pairwise protein profile similarity using jaccard metric.
dice	if TRUE, computes pairwise protein profile similarity using dice measure.
apex	If TRUE, computes pairwise protein profile similarity using apex.
minfo	If TRUE, computes pairwise protein profile similarity using mutual information.
bayesian	If TRUE, computes pairwise protein profile similarity using Bayes correlation based on zero-count distribution.
wcc	If TRUE, computes pairwise protein profile similarity using weighted cross correlation.
euclidean	if TRUE, computes pairwise protein profile similarity using euclidean measure.
manhattan	if TRUE, computes pairwise protein profile similarity using manhattan measure.
canberra	if TRUE, computes pairwise protein profile similarity using canberra measure.
avg.distance	if TRUE, computes pairwise protein profile similarity using avg.distance measure.
rept	Poisson iterations, defaults to 10.
corr_removal	If TRUE, removes protein pairs with correlation scores < the user defined threshold ; defaults to FALSE.
corr_cutoff	user defined threshold for correlation similarity scores. Defaults to 0.5.

Details

calculate_PPIscore

Value

A data frame containing the calculated features for all possible protein pairs.

Author(s)

Matineh Rahmatbakhsh, [e-mail]

Examples

M1<-matrix(rnorm(36),nrow=6)
M1 <- abs(M1)
rownames(M1) <- c("A","B","C","D","E","F")
scored_Data <- calculate_PPIscore(M1)

MACP documentation built on March 7, 2023, 7:42 p.m.