RRHO2_initialize: RRHO2

In RRHO2/RRHO2: improved RRHO package

RRHO2

Description

An improved version for RRHO, which aims to correct the intepretation for top left region (up in x and down in y) nad bottom right region.

Usage

RRHO2_initialize(
  list1,
  list2,
  stepsize = defaultStepSize(list1, list2),
  labels = NULL,
  log10.ind = FALSE,
  multipleTesting = "none",
  boundary = 0.1,
  method = "hyper"
)

Arguments

list1	data.frame. First column is the element (possibly gene) identifier, and the second is its value on which to sort. For differential gene expression, values are often -log10(P-value) * sign(effect).
list2	data.frame. Same as list1.
stepsize	Controls the resolution of the test: how many items between any two overlap tests.
labels	A two element vector indicating the label of list1 and list2.
log10.ind	Logical. Should pvalues be reported and plotted in -log10 scale and not -log scale?
multipleTesting	Three options. none: raw p-value; BH: BH correction; BY: BY correction.
boundary	Size of the white strip. 0.1 indicates 10% of the heatmap size.
method	Method for odds ratio or pvalue representation "fisher" used odds ratio and "hyper" uses p-value.

Details

We improved the algorithm such that all four regions of RRHO plot are meaningful

Value

list of result

hypermat	Matrix of -log(pvals) of the test for the first i,j elements of the lists##' the overlapping test between the first ith element of the sorted list1, using the Stratified representation.
genelist_uu	Genes are are up-regulated in list 1 and up-regulated list 2, at the most significant pixel of the uu quadrant
genelist_dd	Genes are are down-regulated in list 1 and down-regulated list 2, at the most significant pixel of the dd quadrant
genelist_du	Genes are are down-regulated in list 1 and up-regulated list 2, at the most significant pixel of the du quadrant
genelist_ud	Genes are are up-regulated in list 1 and down-regulated list 2, at the most significant pixel of the ud quadrant

Author(s)

Kelly and Caleb

Examples

## A total of 2000 genes in both list 1 and list 2.
## In list 1, genes 1-200 are up-regulated; genes 201-400 are down-regulated; the rest of the 1600 genes are noise genes. 
## In list 2, genes 1-200 are up-regulated; genes 201-400 are down-regulated; the rest of the 1600 genes are noise genes.  

set.seed(15213)
nGenes <- 2000
nDE <- 200
Genes <- paste0("Genes",1:nGenes)

list1_pvalue_1_200 <- runif(nDE,0,0.05)
list1_pvalue_201_400 <- runif(nDE,0,0.05) 
list1_pvalue_401_2000 <- runif(nGenes - 2 * nDE,0,1)
list1_DDE <- c(-log10(list1_pvalue_1_200), -log10(list1_pvalue_201_400) * (-1), -log10(list1_pvalue_401_2000) * sample(c(1,-1), length(list1_pvalue_401_2000), replace = TRUE))

gene_list1 <- data.frame(Genes=Genes,DDE = list1_DDE, stringsAsFactors = FALSE)

list2_pvalue_1_200 <- runif(nDE,0,0.05)
list2_pvalue_201_400 <- runif(nDE,0,0.05) 
list2_pvalue_401_2000 <- runif(nGenes - 2 * nDE,0,1)
list2_DDE <- c(-log10(list2_pvalue_1_200), -log10(list2_pvalue_201_400) * (-1), -log10(list2_pvalue_401_2000) * sample(c(1,-1), length(list2_pvalue_401_2000), replace = TRUE))

gene_list2 <- data.frame(Genes=Genes,DDE = list2_DDE, stringsAsFactors = FALSE)

RRHO_obj <-  RRHO2_initialize(gene_list1, gene_list2, labels = c("list1", "list2"), log10.ind=TRUE)

RRHO2/RRHO2 documentation built on March 22, 2022, 12:04 p.m.