ttsDE

ttsDE, A tail-based test statistics (TTS) for differentially expression detection (Paper submitted).

TTS is a tail-based test to identify diffentially expressed genes between two groups. TTS is a quantile-based model that takes expression values at exon level, and adjusts for covariates.

Installation

In R,

devtools::install_github("SkadiEye/ttsDE")

Example

library(ttsDE)
## Load LUAD data
data("LUAD")

set.seed(4321)
## Run TTS on LUAD data, tau = 0.5
(a <- Sys.time()) 

## [1] "2020-07-01 23:28:22 EDT"

mod1 <- ttsDE(LUAD$z, LUAD$d, LUAD$c, gene = LUAD$gene, tau = 0.5, method = "TTS")

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(b <- Sys.time() - a)

## Time difference of 5.641908 mins

## Run TTS on LUAD data using 8 cores
(a <- Sys.time()) ## 1.275387 mins

## [1] "2020-07-01 23:34:00 EDT"

mod8 <- ttsDE(LUAD$z, LUAD$d, LUAD$c, gene = LUAD$gene, tau = 0.5, method = "TTS", n_core = 8)
(b <- Sys.time() - a)

## Time difference of 1.180652 mins

library(ggplot2)
ggplot(data.frame(gene = levels(LUAD$gene), `-log10(p)` = -log10(mod8$TTS), check.names = FALSE), 
       aes(x = gene, y = `-log10(p)`)) + geom_point(na.rm = TRUE) + theme_classic()