# Quality Control for RNA-Seq Data

## Documentation for package ‘RNAseqQC’ version 0.2.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

all_numeric | for a vector x, check if all non-NA elements of x can be converted to numeric
filter_genes | Filter genes with low counts
get_gene_id | Get all gene IDs in a DESeqDataSet for a given gene name.
make_dds | Make DESeqDataSet from counts matrix and metadata
mean_sd_plot | Create a mean-sd plot Make a scatterplot that shows for each gene its standard deviation versus mean.
plot_biotypes | Plot number of counts per sample and biotype
plot_chromosome | Plot gene expression along a chromosome
plot_gene | Plot a gene
plot_gene_detection | Plot number of detected genes for each sample
plot_library_complexity | Plot the library complexity
plot_loadings | Plot loadings of a principal component
plot_ma | MA-plot of a differential testing result
plot_pca | Plot results of a principal component analysis
plot_pca_scatters | Plot matrix of PCA scatter plots
plot_sample_clustering | Plot clustering of samples in a distance heatmap
plot_sample_MAs | MA plots of samples
plot_total_counts | Plot total counts per sample
plot_within_level_sample_MAs | Plot correlations of samples within a level of a group
save_plots_to_pdf | Save list of plots to PDF
T47D | The T47D cell line data of RNA-seq experiment GSE89888
T47D_diff_testing | Differential expression results corresponding to the T47D data set.