edgefinder: Detect edges in co-expression datasets.

In haimbar/edgefinder: Detect Edges in Sparse Co-expression Graphs

Description

Fit the L2N model to normalized correlation coefficients between pairs of genes. The mixture model has three component - the null component follows a normal distribution, and the two non-null components follow lognormal distributions. An edge is in the graph if the correlation between the two end-point genes is large enough and determined to be in one of the non-null components.

Usage

edgefinder(
  Exprs,
  BHthr = 0.01,
  rndseed = 112211,
  maxLen = 20000,
  LOvals = 30,
  ttl = "",
  trim = 0,
  verbose = FALSE,
  plot.it = FALSE
)

Arguments

Exprs	A numeric matrix with normalized gene expression data. Rows correspond to genes, and columns correspond to samples.
BHthr	the Benjamini-Hochberg fasle discovery rate threshold to be used to determine which pairs are strongly correlated. Default=0.01.
rndseed	The random seed used to select a subset of the pairs.
maxLen	The maximum number of pairs that will be randomly selected to fit the L2N model. Default=20000.
LOvals	the maximum log-odds ratio to be used to determine the cut-off points to declare which correlations are significant. The program will check which log-odds ratio (1,2,...,LOvals) results in FDR less than or equal to the user-specified BHthr. Default=30.
ttl	Title for the fitted-model plot. Default=""
trim	Fraction of extreme values to exclude from the fitted-model plot. Default=0 (show all the data).
verbose	Whether to show progress message to the user. Default=FALSE.
plot.it	Whether to show the fitted mixture plot to the user. Default=FALSE.

Value

A list with the following elements

• G The total number of genes.

• p1 The proportion of genes in the right mixture component (positively correlated.)

• p2 The proportion of genes in the left mixture component (negtively correlated.)

• p0 The proportion of genes in the null component (un-correlated.)

• m0, m1, m2, s0, s1, s2 The location and scale parameters of the three mixture components.

• thrtable A table with 6 columns: posterior probability ratio (ppr) between the non-null components and the null component), the right component cutoff corresponding to the ppr, the left component cutoff, the estimated probability of Type-I errors, the estimated power, the estimated FDR.

• LogOddsRatio The log-odds ratio that yields FDR closest to the desired level.

• fitted The fitted model (as returned by the EM function).

• rmse The root mean-squared error of the fitted model.

• rt, lt The significant edges (from the right and left mixture components.)

• AdjMat The (sparse) adjacency matrix with edges corresponding to rt, lt.

Examples

   data(WT)
   WTres <- edgefinder(WT, ttl = "Wild Type")

haimbar/edgefinder documentation built on Dec. 20, 2021, 2:45 p.m.