Overview

Today we’ll be going over R functions, but will start off with some file reading first.

plot(1:10, type = 'l', col = 'blue')

test1 file

test1 <- read.table('test1.txt', header = T, sep = ',')
test1

##   Col1 Col2 Col3
## 1    1    2    3
## 2    4    5    6
## 3    7    8    9
## 4    a    b    c

test2 file

test2 <- read.table('./test2.txt', sep = '$', header = T)
test2

##   Col1 Col2 Col3
## 1    1    2    3
## 2    4    5    6
## 3    7    8    9
## 4    a    b    c

test3 file

test3 <- read.table('./test3.txt', header = F)
test3

##   V1 V2 V3
## 1  1  6  a
## 2  2  7  b
## 3  3  8  c
## 4  4  9  d
## 5  5 10  e

First function

add <- function(x, y = 1) {
  # the body
  x + y
}

add(c(1, 3, 5))

## [1] 2 4 6

# add(1, 3, 5)
# add(x = 1, y = "barry")

rescale <- function(x) {
  rng <- range(x)
  (x - rng[1]) / (rng[2] - rng[1])
}

rescale2 <- function(x, na.rm = T) {
  rng <- range(x, na.rm = na.rm)
  (x - rng[1]) / (rng[2] - rng[1])
}

x <- c(1:10, NA)
rng <- range(x)
(x - rng[1]) / (rng[2] - rng[1])

##  [1] NA NA NA NA NA NA NA NA NA NA NA

rng

## [1] NA NA

print(rescale2(c(1:10, NA)))

##  [1] 0.0000000 0.1111111 0.2222222 0.3333333 0.4444444 0.5555556 0.6666667
##  [8] 0.7777778 0.8888889 1.0000000        NA

print(rescale2(c(1:10, NA), na.rm = F))

##  [1] NA NA NA NA NA NA NA NA NA NA NA

Another example extension…

rescale3 <- function(x, na.rm=TRUE, plot=FALSE) {
  rng <-range(x, na.rm=na.rm)

  print("Hello")
  answer <- (x - rng[1]) / (rng[2] - rng[1])
  print("is it me you are looking for?")
  if(plot) {
    plot(answer, typ="b", lwd=4)
    print("Don't sing please!!!!")
  }
  print("I can see it in ...")
  return(answer)
}

rescale3(1:10)

## [1] "Hello"
## [1] "is it me you are looking for?"
## [1] "I can see it in ..."

##  [1] 0.0000000 0.1111111 0.2222222 0.3333333 0.4444444 0.5555556 0.6666667
##  [8] 0.7777778 0.8888889 1.0000000

rescale3(1:10, plot = T)

## [1] "Hello"
## [1] "is it me you are looking for?"

## [1] "Don't sing please!!!!"
## [1] "I can see it in ..."

##  [1] 0.0000000 0.1111111 0.2222222 0.3333333 0.4444444 0.5555556 0.6666667
##  [8] 0.7777778 0.8888889 1.0000000

Practical protein interaction example

source('./bio3d_example.R', echo = T)

## 
## > require(bio3d)

## Loading required package: bio3d

## 
## > prot_interact <- function(pdb.name, chain = "A", elety = "CA", 
## +     ret = F) {
## +     pdb.dat <- read.pdb(pdb.name)
## +     chain <- trim.pdb(pdb.dat .... [TRUNCATED]

prot_interact

## function (pdb.name, chain = "A", elety = "CA", ret = F) 
## {
##     pdb.dat <- read.pdb(pdb.name)
##     chain <- trim.pdb(pdb.dat, chain = chain, elety = elety)
##     chain.b <- chain$atom$b
##     plotb3(chain.b, sse = chain, typ = "l", ylab = "Bfactor")
##     if (ret) {
##         return(chain.b)
##     }
## }

int1 <- prot_interact('4AKE', ret = T)

##   Note: Accessing on-line PDB file

int2 <- prot_interact('1AKE', ret = T)

##   Note: Accessing on-line PDB file
##    PDB has ALT records, taking A only, rm.alt=TRUE

int3 <- prot_interact('1E4Y', ret = T)

##   Note: Accessing on-line PDB file

hc <- hclust( dist( rbind(int1, int2, int3) ) )
plot(hc)