R/polishCPs.R

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

polishCPs <- function(CPs){
    proximal.apa.len <- sapply(CPs$Predicted_Proximal_APA, length)
    CPs$Predicted_Proximal_APA[proximal.apa.len==0] <- 
        ifelse(CPs$dCPs$type[proximal.apa.len==0]=="novel proximal", # else== novel distal
               CPs$idx1[proximal.apa.len==0],
               CPs$saved.id[proximal.apa.len==0])
    coors <- lapply(CPs$chr.cov.merge, function(.ele) as.numeric(rownames(.ele)))
    flag <- CPs$flag
    CPs$fit_value[flag] <- mapply(function(cov_diff, idx){
        ifelse(is.na(idx[1]) | is.null(idx[1]), NA, cov_diff[idx[1]])
    }, CPs$fit_value[flag], 
    CPs$Predicted_Proximal_APA[flag], 
    SIMPLIFY=FALSE)
    CPs$Predicted_Proximal_APA <- mapply(function(.ele, .id){
        ifelse(is.na(.id[1]) | is.null(.id[1]), NA, .ele[.id[1]])
    }, coors,
    CPs$Predicted_Proximal_APA,
    SIMPLIFY=FALSE)
    CPs$fit_value[sapply(CPs$fit_value, length)==0] <- NA
    CPs$dCPs$fit_value <- unlist(CPs$fit_value)
    CPs$Predicted_Proximal_APA[sapply(CPs$Predicted_Proximal_APA, length)==0] <- NA
    CPs$dCPs$Predicted_Proximal_APA <- unlist(CPs$Predicted_Proximal_APA)
    CPs$dCPs[, c("fit_value", "Predicted_Proximal_APA", 
                 "Predicted_Distal_APA", "utr3start", 
                 "utr3end", "type")]
}