isoLQNO: Differential expression between two groups using LQNO model
In lpantano/scounts: Analyze small RNA-seq count data

Description Usage Arguments Details Value Author(s) References Examples

Differential expression between two groups using LQNO model

1	isoLQNO(counts, groups = NULL, long = FALSE)

`counts`	Count matrix.
`groups`	Character vector to indicate the group of each sample.
`long`	Whether matrix is in long format. Default FALSE.

Methods adapted from Argyropoulos et al (2017).

data.frame with estimates and p-values.

Christos Argyropoulos and Lorena Pantano

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

options(warn = -1) # this is only for tiny example
data(dat286)
datRat<-subset(dat286.long,(Series=="Equi" | Series =="RatioA") & Amount=="100 fmoles")
datRat$SampleID<-factor(datRat$SampleID)
datRat$Series<-factor(datRat$Series)
res <- isoLQNO(datRat, long=TRUE)