Differential expression between two groups using LQNO model

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

Arguments

counts

Count matrix.

groups

Character vector to indicate the group of each sample.

long

Whether matrix is in long format. Default FALSE.

Value

data.frame with estimates and p-values.

Details

Methods adapted from Argyropoulos et al (2017).

References

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

Examples

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)