corOrt: Calculate ortholog gene correlation coefficients

Description Usage Arguments Details Value Bibliography See Also Examples

Description

Calculate correlation between sets of matched orthologous genes using either method from Takao et al. (2015) or Seok et al. (2013)

Usage

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corOrt(x, g = NULL, pval = 0.05, lfc = 0)

Arguments

x

an object of class matchedOrtholog

g

either a vector of gene names of genes of interest, or an object of class "tmod" with definitions of modules. If NULL, all genes will be used

pval

p value threshold

lfc

log_2 fold change threshold

Details

This function calculates Pearson Correlation, squared Pearson correlation and Spearman correlation for mouse and human logFC values for genes with significant p-values for differential regulation. As in PNAS 2013 110 (9) 3507-3512, for the calculation of squared Pearson correlation coefficient all the genes that are significantly regulated in at least one specie are taken into account, while for the calculation of Spearman's correlation coefficient only the genes significantly regulated in both species as in PNAS 2015 112 (4) 1167-1172.

The parameters can be calculated either for all genes in the orthologs object, for an explicit list of genes as a character vector parameter g, or for a set of tmod modules, if the parameter g is an object of class tmod.

Value

corOrt returns a data frame with the following columns:

r

Pearson correlation coefficient r

Seok

correlation measure described by Seok et al. – squared Pearson r correlation coefficient for genes significantly up- or downregulated in one of the two orthologous sets

Seok.N

number of gene pairs that were used to calculate the Seok coefficient

rho

Spearman correlation coefficient rho

Takao

correlation measure described by Takao et al. – Spearman correlation coefficient for genes significantly up- or downregulated in both of the two gene orthologous sets

Takao.N

number of gene pairs that were used to calculate the Takao coefficient; smaller or equal to Seok.N

N

total number of gene pairs in the given gene set

Bibliography

Seok, Junhee, et al. "Genomic responses in mouse models poorly mimic human inflammatory diseases." Proceedings of the National Academy of Sciences 110.9 (2013): 3507-3512.

Takao, Keizo, and Tsuyoshi Miyakawa. "Genomic responses in mouse models greatly mimic human inflammatory diseases." Proceedings of the National Academy of Sciences 112.4 (2015): 1167-1172.

See Also

modCor

Examples

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library(tmod)
data(tmod)
data(orthologs)
a <- corOrt(orthologs)
disco <- disco.score(orthologs)
ord <- order(disco, decreasing = TRUE)
concordant <- tmodCERNOtest(toupper(orthologs$genes)[ord])
corOrt(orthologs, g=tmod[concordant$ID])

disco documentation built on May 2, 2019, 9:40 a.m.