counts: Display expected and observed counts of co-significant genes
In alexploner/VEGAStools: Basic manipulations of VEGAS gene lists

Description Usage Arguments Details Value

Given two gene lists of class VEGAS and a p-value threshold, this function reports the number of genes below this threshold on both lists, with a 95% confidence interval for the true value, as well as the the expected number under the null hypothesis of no association between the gene lists, and the corresponding p-value

counts(x, y, co = 0.05, adjusted = FALSE)

plotCounts(x, y, minP = 1e-06, maxP = 0.1, nP = 100, adjusted = FALSE,
  legend = TRUE, ylim, title, xlab, ylab, ...)

`x,y`	Two gene lists of class `VEGAS`
`co`	Cutoff for selecting statistically significant genes in both lists
`adjusted`	Logical flag indicating whether to use the raw or adjusted p-values (default: `FALSE`).
`minP,maxP`	Smallest and largest cutoff value for considering the overlap in significant genes between lists
`nP`	Number of intermediate points between `minP` and `maxP`
`legend`	Logical flag indicating whether to add a legend to the plot
`ylim,title,xlab,ylab,...`	Standard graphical prarameters for `plot` to override the function defaults

Confidence intervals, expected count and p-value are based on binom.test. The expected count under the null hypothesis is conditional on the p-values observed for each trait individually, i.e. we assume that the probability to be significant on both lists is the product of the marginal proportions of significant genes on each list. Warning: inference assumes independence between genes, which is a rather strong assumption in this setting.

counts returns a named vector with five components: Obs, the number of genes observed to be statistically significant on both lists at the chosen cutoff, LCL and UCL, the corresponding confidence interval for the number of overlapping genes, Exp, the number of genes expected to be significant on both lists under the assumption of no association between the underlying traits, and p.value, the corresponding two-sided p-value.

plotCounts generates a plot of observed/expected counts as a function of the specified cutoff range and returns invisibly a data frame with the cutoffs (column co) and the corresponding output from counts.

alexploner/VEGAStools documentation built on May 10, 2019, 8:57 a.m.