This is the source file for fitting the linear quadratic normal family
isoCorrect(train, data, cycles = 5000, long = FALSE)
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). |
data.frame with corrected expression
Methods adapted from:
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(mirTritation) ma <- isoCorrect(mirTritation[mirTritation$class=="train",], mirTritation[mirTritation$class=="test",],cycles=5,long=TRUE)#> GAMLSS-RS iteration 1: Global Deviance = 39000 #> GAMLSS-RS iteration 2: Global Deviance = 38564 #> GAMLSS-RS iteration 3: Global Deviance = 37919 #> GAMLSS-RS iteration 4: Global Deviance = 36918 #> GAMLSS-RS iteration 5: Global Deviance = 35390 #> GAMLSS-RS iteration 1: Global Deviance = 9211 #> GAMLSS-RS iteration 2: Global Deviance = 8003 #> GAMLSS-RS iteration 3: Global Deviance = 7217 #> GAMLSS-RS iteration 4: Global Deviance = 6800 #> GAMLSS-RS iteration 5: Global Deviance = 6580