Saving_loading_if_for_apply.Rmd

---
title: "Saving_loading_if_for_apply"
author: "Chengqi(Charley) Wang"
date: "1/29/2020"
output: html_document
---
<br/><br/>


####Load the RNA-Seq data
```{r}
##set your working directory and load the data
setwd('~/Documents/work/paper_write/genome_training/R_training/')
df <- read.table('vehicle_drug_feature_counts.txt',
                 header = T, sep = '\t', row.names = 1)
summary(df)
df <- df[,6:9]
```
<br/><br/>

####Save the data
```{r}
write.table(df, 
            file = 'vehicle_drug_feature_counts.copy.txt.txt', #either a character string naming a file or a connection open for writing. "" indicates output to the console.
            row.names = T, #indicating whether the row names of df are to be written
            col.names = T, #indicating whether the column names of df are to be written
            sep = '\t',    #the field separator string
            quote = F      #a logical value (TRUE or FALSE) or a numeric vector. If TRUE, any character or factor columns will be surrounded by double quotes.
            )

###load again
df2 <- read.table('vehicle_drug_feature_counts.copy.txt.txt',header = T, sep = '\t', row.names = 1)
head(df2)
```
<br/><br/>

#### 'For' loop
```{r}
df <- as.matrix(df)
##check the quantile for each assay
for (i in 1:ncol(df))
{
   print(  colnames(df)[i] )
   qu <- quantile( df[, i] )
   print(qu)
}
```
<br/>

#### 'Apply' replaces 'for' loop
```{r}
qu <- apply(df, 2, function(z){quantile(z)})
print(qu)
```
<br/>

#### if...else statement
```{r}
### pick the expressed genes in first assay
exp_cutoff   <- quantile(df[,1], 0.35)
unEXP_cutoff <- quantile(df[,1], 0.3)
n_remaining  <- 0
exp_gene   <- c() #set a empty vector for expressed genes
unexp_gene <- c() #set a empty vector for un_expressed genes
for (i in (1:length(df[,1])))
{
    if (df[i, 1] > exp_cutoff  )
    {
        exp_gene <- c(exp_gene, rownames(df)[i])  
    }
    else if (df[i, 1] < unEXP_cutoff) 
    {
        unexp_gene <- c(unexp_gene, rownames(df)[i])
    }
    else
    {
        n_remaining <- n_remaining + 1    
    }
}

print(c(length(unexp_gene),
      length(exp_gene),
      n_remaining))
```

<br/>

####use 'which' to replace former script
```{r}
exp_gene2 <- rownames(df)[which(df[,1] > exp_cutoff)]
length(exp_gene2)
length(exp_gene)
```