calculate.rho.signed: correlation calculation

In songw01/MEGENA: Multiscale Clustering of Geometrical Network

correlation calculation

Description

correlation analysis with FDR calculation

Usage

calculate.rho.signed(datExpr,n.perm = 10,FDR.cutoff = 0.05,estimator = "pearson",
                               use.obs = "na.or.complete",
                               direction = "absolute",
                               rho.thresh = NULL,sort.el = TRUE)

Arguments

datExpr	gene expression data matrix
n.perm	Number of permutations to perform. If doPerm = NULL, calculates BH FDR p-values instead of permutation based FDR.
FDR.cutoff	FDR threshold to output final results of significant correlations.
estimator	Type of correlation coefficient to calculate, and gets passed to 'method' in 'cor()' function. Either "pearson" or "spearman".
direction	If direction = "absolute", absolute valued correlations are considered. If direction = "positive" or "negative", signed correlation is considered, and significance is calculated for positive/negative values.
rho.thresh	vector of correlation cutoff threshold to calculate significance. If NULL, threshold values will be generated by increment of 0.01 between -1 and 1 (if direction = "positive" or "negative"), or 0 and 1 (if direction = "absolute").
sort.el	logical value to determine whether correlation list should be sorted
use.obs	an optional character string giving a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs".

Details

direction = "absolute" can serve as two-tailed significance test, where as direction = "positive"/"negative" is one-tailed test.

Value

output is a list. output$signif.ijw is three column edgelist data.frame, third column being the weight. output$FDR is the permutation FDR table across the threshold values in rho.thresh.

Author(s)

Won-Min Song

Examples

data(Sample_Expression)
rho.out = calculate.rho.signed(datExpr,n.perm = 10,FDR.cutoff = 0.05,estimator = "pearson",
                               use.obs = "na.or.complete",
                               direction = "absolute",
                               rho.thresh = NULL,sort.el = TRUE)

songw01/MEGENA documentation built on Jan. 19, 2024, 6:51 p.m.