handout.md

# welcome
- introduction (previous coding experiment, goal)
- schedule
  - first day: the basics, (boring but essential)
  - second day: visualization
  - third day: follow on an online tutorial
  
- posit
 - r & rstudio 

# first day
## about interface
 - different panels
 - scripts: run, save, open
 - setting working directory
 - console
 - notebook
 
`?sqrt`

"=" versus "<-"

`?sample`

```
data <- rnorm(1000)
quantiles <- quantile(data, probs = c(0, 0.25, 0.5, 0.75, 1))
quantiles
```

hopefully, lunch break before `Basic table functions`

# second day
skip the part of own function of volcano plot

# third day
## looking at data
```
airway
assays(airway)
rowData(airway)
colData(airway) #sample_table.csv
talking about the data structure
```
## loading data

`read.csv( file.path(indir, "SraRunInfo_SRP033351.csv"))`

bamfiles:
```
library('Rsamtools')
#scanBam() will only read yieldSize number of alignments
scanBam(BamFile(filenames[1],yieldSize = 200))
```

## Exploratory analysis and visualization
spend time on reading why transformation is needed and what are the challenges

## DEGs
spend time on reading the normalization method

```
res@elementMetadata@listData$description
mcols(res, use.names = TRUE)
res[order(res$padj),]
```