Function reference • llfsRnaseq

Handling Raw Data These functions assist with running the nf-core/rnaseq pipeline and handling the output
`combine_txi_objects()`	combine two txi objects
Sex Mislabe QC Functions These functions are used in the Sex Mislabelling QC Vignette
`sex_mislabel_setup()`	set up the QC notebook with the data sets which are used throughout
`top_500_pca_for_sex_mislabels()`	Use the top 500 most variable genes to calculate PCs and infer sex
Batch Effect QC Functions These functions are used in in the Batch Effects QC Vignette
`batch_effect_qc_setup()`	set up the QC notebook with the data sets which are used throughout
`before_after_pca_and_plate_regression_plots()`	Before and After PCA and Plate Regression Plots
`direction_change_in_percent_intergenic()`	make a plot showing the direction of percent intergenic on PC1/2 axis
`filter_dds_restimate_sizeFactors()`	Apply boolean vector filtering on the columns and/or rows and return filtered DDS object with size factors
`project_counts_onto_orig_pcs()`	Project counts, presumably with some effect removed, onto different PCs
`remove_parameter_effects()`	remove coefficient effects from counts
Variant Comparison Functions used to compare RNA variant and WGS data
`parse_all_by_all_compiled_results()`	summarize an all_by_all_compiled_metrics dataframe for upload to the database

Reference