Multiple QC Reports

#Knitr settings
knitr::opts_chunk$set(
  warning=FALSE, message=FALSE, echo=TRUE, tidy=FALSE, error=FALSE,
  fig.show='hold', fig.width=3.5, fig.height = 3.5
)
options(width=150)
if(is.null(experiment)) experiment <- "Sequencing data"

Required R packages

library(fastqcr)
library(dplyr)

Aggregating Reports

qc <- qc_aggregate(qc.path, progressbar = FALSE)
qc

Column names:

```{block, type = "block"}
The table shows, for each sample, the names of tested FastQC modules, the status of the test, as well as, some general statistics including the number of reads, the length of reads, the percentage of GC content and the percentage of duplicate reads.

## Summary

```r
summary(qc)

Column names:

```{block, type = "block"} The table shows, for each FastQC module, the number and the name of samples that failed or warned.

## General statistics


```r
qc_stats(qc)

Column names:

```{block, type = "block"} The table shows, for each sample, some genral statistics such as the total number of reads, the length of reads, the percentage of GC content and the percentage of duplicate reads

## Inspecting Problems

### Failed modules in the most samples


```r
qc_fails(qc, "module")

```{block, type = "block"} For each module, the number of problems (failures) and the name of samples, that failed, are shown.

### Warned module in the most samples


```r
qc_warns(qc, "module")

Samples with Problems

qc_problems(qc, "sample")
qc_problems(qc, "sample", compact = FALSE)


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fastqcr documentation built on March 7, 2023, 8:16 p.m.