PEA-m5C: Predicting m5C sites by PEA-m5C
In cma2015/PEA-m5C: An integrated R toolkit for plant m5C analysis.

Description Usage Arguments Value Author(s) Examples

Predicting m5C modification sites based on PEA-m5C. PEA-m5C provide four threshold (VHmode: very high confidence with specificity of 99 precent; HMode: high confidence mode with specificity of 95 precent; NMode: normal confidence with specificity of 90 precent; LMode: low confidence mode with specificity of 85 precent) to meet different requirements.

1	predict_m5c(sample_feature,mode=NULL)

`sample_feature`	A dataframe or list of RNA sequence.
`mode`	A string character of .

A matrix with 4 columns including transcripts ID, candidate m5C position, probabilistic scores for being m5C and which mode of m5C.

Jie Song, Jingjing Zhai, Chuang Ma

aaa <- extra_motif_seq(input_seq_dir = paste0(system.file(package = "PEAm5c"),"/data/cdna.fa"),up = 5)
aaa <- lapply(aaa, c2s)
bbb <- FeatureExtract(aaa)
ccc <- predict_m5c(bbb)