isoCorrect: Correct miRNA expression based on prior ligation bias...

In lpantano/scounts: Analyze small RNA-seq count data

Description

This is the source file for fitting the linear quadratic normal family

Usage

isoCorrect(train, data, cycles = 5000, long = FALSE)

Arguments

train	Long data.frame to train model.
data	Long data.frame to correct abundance.
cycles	Number of cycles to reach convergency.
long	Boolean if input is in long format instead of standard wide format (rows:miRNAs, columns:samples).

Details

Methods adapted from:

Argyropoulos, Christos, et al. "Modeling bias and variation in the stochastic processes of small RNA sequencing." Nucleic Acids Research (2017).

Value

data.frame with corrected expression

Author(s)

Christos Argyropoulos and Lorena Pantano

Examples

options(warn = -1) # this is only for tiny example
data(mirTritation)
ma <- isoCorrect(mirTritation[mirTritation$class=="train",],
mirTritation[mirTritation$class=="test",],cycles=5,long=TRUE)
library(ggplot2)
ggplot(ma,aes(y=log2(reads), x=Dilution)) + geom_jitter()
ggplot(ma,aes(y=m, x=Dilution)) + geom_jitter()

lpantano/scounts documentation built on May 27, 2019, 2:01 a.m.