computeProteinPI: protein pI computation

In PengyiYang/ReFraction: A machine learning approach for deterministic identification of protein homologues and splice variants in large-scale MS-based proteomics

Usage

computeProteinPI(keyAA)

Arguments

keyAA

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (keyAA) 
{
    AspNumber <- keyAA[1]
    GluNumber <- keyAA[2]
    CysNumber <- keyAA[3]
    TyrNumber <- keyAA[4]
    HisNumber <- keyAA[5]
    LysNumber <- keyAA[6]
    ArgNumber <- keyAA[7]
    NQ <- 0
    QN1 <- 0
    QN2 <- 0
    QN3 <- 0
    QN4 <- 0
    QN5 <- 0
    QP1 <- 0
    QP2 <- 0
    QP3 <- 0
    QP4 <- 0
    pH <- 6.5
    pHprev <- 0
    pHnext <- 14
    X <- 0
    E <- 0.01
    temp <- 0
    tabl <- 650
    while (TRUE) {
        QN1 <- tab[tabl, 1]
        QN2 <- -AspNumber/tab[tabl, 2]
        QN3 <- -GluNumber/tab[tabl, 3]
        QN4 <- -CysNumber/tab[tabl, 4]
        QN5 <- -TyrNumber/tab[tabl, 5]
        QP1 <- HisNumber/tab[tabl, 6]
        QP2 <- tab[tabl, 7]
        QP3 <- LysNumber/tab[tabl, 8]
        QP4 <- ArgNumber/tab[tabl, 9]
        NQ <- QN1 + QN2 + QN3 + QN4 + QN5 + QP1 + QP2 + QP3 + 
            QP4
        if (NQ < 0) {
            temp <- pH
            pH <- pH - ((pH - pHprev)/2)
            pHnext <- temp
        }
        else {
            temp <- pH
            pH <- pH + ((pHnext - pH)/2)
            pHprev <- temp
        }
        if ((pH - pHprev < E) & (pHnext - pH < E)) {
            break
        }
        n <- pH * 100
        obc <- n
        ulamek <- n - obc
        if (ulamek >= 0.5) {
            obc <- obc + 1
        }
        tabl <- obc
        pH <- obc
        pH <- pH/100
    }
    return(pH)
  }

PengyiYang/ReFraction documentation built on May 14, 2019, 11:01 p.m.