BamstoCountMatrixviaFeatureCounts.Rmd

---
title: "Bam to Counts Notebook"
output:
  html_document:
    df_print: paged
---


```{r}
library(Rsubread)
```


# Feature counts
```{r}
# GTF File
gtf_file <- "C:/Users/kesha/Documents/R/Rtuts/Data/WG__Discussion_Alina's_EPEC_project/bam/Mus_musculus.GRCm38.102.gtf"
```

```{r}
# Bam files
bam_path <- "C:/Users/kesha/Documents/R/Rtuts/Data/WG__Discussion_Alina's_EPEC_project/bam/"
bamFiles <- list.files(bam_path, pattern = ".*bam$")
bamFiles
```

```{r}
#setwd(bam_path)
# specifying the gtf file containing the annotations and the format of the file
# counting reads that match overlap exons and grouping exons by gene_id
count_matrix <- featureCounts(files = bamFiles , GTF.featureType="exon",
                              GTF.attrType="gene_id",annot.ext= gtf_file, 
                              isGTFAnnotationFile=TRUE, isPairedEnd=FALSE) 
```


```{r}
count_matrix
```




```{r}
summary(count_matrix)
```
counts refers to the total number of unique genes that was in the GTF file used for counting,
annotation refers to the genomic location of each feature being counted, 
targets are the input samples, and 
stat is the summary of how many reads are being used for counting.


```{r}
sample_ID <- colnames(count_matrix$counts) 
print(sample_ID)
```

Finally, as a good practice, always save the R image to your working directory
```{r}
path <- "C:/Users/kesha/Documents/R/Rtuts/Data/WG__Discussion_Alina's_EPEC_project/"
save.image(paste0(path, "/featureCounts_workspace", ".RData"))

```

# take a loook at objcts inside count matrix

```{r}
names(count_matrix)
```
```{r}
count_matrix$stat
```

The counts for the samples are stored in fc$counts. Take a look at that.

```{r}
## Take a look at the dimensions to see the number of genes
dim(count_matrix$counts)
```
Take a look at a small set of values

```{r}
head(count_matrix$counts, 10)
```

```{r}
count_matrix$targets
```



The annotation slot shows the annotation information that featureCounts used to summarise reads over genes.
```{r}
Gene_ID <- count_matrix$annotation
head(Gene_ID, 10)
```

```{r}
counts <- write.csv(
  count_matrix$counts,
  "C:/Users/kesha/Documents/R/Rtuts/Data/WG__Discussion_Alina's_EPEC_project/fc/counts.csv"
)
annotations <- write.csv(
  count_matrix$annotation,
  "C:/Users/kesha/Documents/R/Rtuts/Data/WG__Discussion_Alina's_EPEC_project/fc/annotation.csv"
)
samples <- write.csv(
  count_matrix$targets,
  "C:/Users/kesha/Documents/R/Rtuts/Data/WG__Discussion_Alina's_EPEC_project/fc/samples.csv"
)
stats_counts <- write.csv(
  count_matrix$stat,
  "C:/Users/kesha/Documents/R/Rtuts/Data/WG__Discussion_Alina's_EPEC_project/fc/stats_counts.csv"
)
```