# gscreend - analysis of pooled CRISPR screens
### Run gscreend, as also explained in the vignette section
Set up a SummarizedExperiment object containing a matrix of raw count data, rowData on gRNAs and genes and colData on the sample type.
```{r}
counts_matrix <- cbind(raw_counts$library0, raw_counts$R0_0, raw_counts$R1_0)
rowData <- data.frame(sgRNA_id = raw_counts$sgrna_id,
gene = raw_counts$Gene)
colData <- data.frame(samplename = c("library", "R1", "R2"),
# timepoint naming convention:
# T0 -> reference,
# T1 -> selected
timepoint = c("T0", "T1", "T1"))
se <- SummarizedExperiment(assays=list(counts=counts_matrix),
rowData=rowData, colData=colData)
```
Create a PoolScreenExp object
```{r}
pse <- createPoolScreenExp(se)
```
Run gscreend
```{r}
pse <- RunGscreend(pse)
```
