createVectors: Create correlation coefficient vectors based on bivariate...

In siskac/discordant: The Discordant Method: A Novel Approach for Differential Correlation

Description

Calculates correlation coefficients based on two groups of -omics bivariate data. Currently, only two groups of samples can be specified. Used to make input for discordantRun().

Usage

createVectors(
  x,
  y = NULL,
  groups,
  cor.method = c("spearman", "pearson", "bwmc", "sparcc")
)

Arguments

x	ExpressionSet of -omics data
y	Optional second ExpressionSet of -omics data, induces dual -omics analysis
groups	n-length vector of 1s and 2s matching samples belonging to groups 1 and 2
cor.method	Correlation method to measure association. Options are "spearman", "pearson", "bwmc" and "sparcc"

Details

Creates vectors of correlation coefficents based on feature pairs within x or between x and y. The names of the vectors are the feature pairs taken from x and y.

Value

List of two named numeric vectors. Vectors give the correlation coefficients for groups 1 and 2 respectively, and vector names give the each feature for the resptive feature pair seperated by an underscore.

Author(s)

Charlotte Siska [e-mail]

Max McGrath [e-mail]

References

Siska C, Bowler R and Kechris K. The Discordant Method: A Novel Approach for Differential Correlation. (2015) Bioinformatics. 32(5): 690-696.

Friedman J and Alm EJ. Inferring Correlation Networks from Genomic Survey Data. (2012) PLoS Computational Biology. 8:9, e1002687.

Examples

## load data
data("TCGA_GBM_miRNA_microarray")
data("TCGA_GBM_transcript_microarray")
print(colnames(TCGA_GBM_transcript_microarray)) # look at groups
groups <- c(rep(1,10), rep(2,20))
# transcript-transcript pairs
vectors <- createVectors(TCGA_GBM_transcript_microarray, 
                         groups = groups, cor.method = c("pearson"))
# miRNA-transcript pairs
vectors <- createVectors(TCGA_GBM_transcript_microarray, 
                         TCGA_GBM_miRNA_microarray, groups = groups)
                         

siskac/discordant documentation built on Feb. 11, 2022, 2:52 p.m.