Quality Control for RNA-Seq Data

Documentation for package ‘RNAseqQC’ version 0.2.1

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.