2.RBasics.rmd

---
title: "R Notebook"
output: html_notebook
---


# 1.12.1 Exercise
```{r}
library()
search()
?vignette
```

```{r}
# to get help on using install.packages
?install.packages

# Note: the parameter is a quoted string!
# install.packages("seqinr",repos="https://cran.rstudio.com/")   
library(help="seqinr") 
library(seqinr)
ls("package:seqinr")
```

```{r}
?seqinr::a # Converts amino-acid three-letter code into the one-letter one
seqinr::a("Tyr")
seqinr::words(3, c("A", "G", "C", "U"))
```
 [1] "AAA" "AAG" "AAC" "AAU" "AGA" "AGG" "AGC" "AGU" "ACA" "ACG" "ACC"
[12] "ACU" "AUA" "AUG" "AUC" "AUU" "GAA" "GAG" "GAC" "GAU" "GGA" "GGG"
[23] "GGC" "GGU" "GCA" "GCG" "GCC" "GCU" "GUA" "GUG" "GUC" "GUU" "CAA"
[34] "CAG" "CAC" "CAU" "CGA" "CGG" "CGC" "CGU" "CCA" "CCG" "CCC" "CCU"
[45] "CUA" "CUG" "CUC" "CUU" "UAA" "UAG" "UAC" "UAU" "UGA" "UGG" "UGC"
[56] "UGU" "UCA" "UCG" "UCC" "UCU" "UUA" "UUG" "UUC" "UUU"
```{r}
aaindex$FASG890101 
aaindex$PONJ960101 
```
```{r}
?data # load dataset
data(aaindex, package="seqinr")   
?aaindex
aaindex$FASG890101 
```
```{r}

```

plot
```{r}
plot(aaindex$FASG890101$I,
     aaindex$PONJ960101$I,
     xlab="hydrophobicity", ylab="volume", type="n")
text(aaindex$FASG890101$I,
     aaindex$PONJ960101$I,
     labels=a(names(aaindex$FASG890101$I)))
```
```{r}
seqinr::choosebank("swissprot")
mySeq <- seqinr::query("mySeq", "N=MBP1_YEAST")
mbp1 <- seqinr::getSequence(mySeq)
seqinr::closebank()
x <- seqinr::AAstat(mbp1[[1]])
barplot(sort(x$Compo), cex.names = 0.6)
```
equivalent preload
```{r}
library(seqinr)
choosebank("swissprot")
mySeq <- query("mySeq", "N=MBP1_YEAST")
mbp1 <- getSequence(mySeq)
closebank()
x <- AAstat(mbp1[[1]])
barplot(sort(x$Compo), cex.names = 0.6)
```
```{r}
library(help = seqinr)       # basic information
browseVignettes("seqinr")    # available vignettes
data(package = "seqinr")     # available datasets
```

```{r}
if (! requireNamespace("sos", quietly=TRUE)) {
    install.packages("sos")
}
library(help = sos)       # basic information
browseVignettes("sos")    # available vignettes
 
sos::findFn("moving average")
```

```{r}
a <- 3
b <- 4
c <- sqrt(a^2 +b^2)
ls()
save(a, file = "tmp.RData")
rm(a)
ls()
load("tmp.RData")
ls()
rm(list=setdiff(ls(), "task_counter"))
ls()
```