m6Aboost {m6Aboost} | R Documentation |
An function for calculating the relative signal strength and extracting all the features that required by the m6Aboost model for each peak.
m6Aboost(object, genome = "", normalization = TRUE)
object |
A GRanges object which should contains all the single nucleotide peaks of miCLIP2 experiment. |
genome |
The name of the BSgenome that you are working with. For example "BSgenome.Mmusculus.UCSC.mm10". |
normalization |
A logical vector which indicates whether you would like normalize the RSS and C to T reads number to the mean value of the training set of the model. This will help to reduce the false positive rate. |
A GRanges object with all the information that is required by the m6Aboost model.
You Zhou
testpath <- system.file("extdata", package = "m6Aboost") test_gff3 <- file.path(testpath, "test_annotation.gff3") test <- readRDS(file.path(testpath, "test.rds")) test<- preparingData(test, test_gff3, colname_reads="WTmean", colname_C2T="CtoTmean") ## The input of m6Aboost should be the output from preparingData function ## Please make sure that the correct BSgenome package have installed ## before running motifProfile. For example, ## library("BSgenome.Mmusculus.UCSC.mm10") test <- m6Aboost(test, "BSgenome.Mmusculus.UCSC.mm10")