Package index • RNASeq Template

Utilities

Partial Residuals

Functions for selectively removing the systematic effect of variables included in a predictive model, to allow patterns that might otherwise be obscured to become apparent.

assemble_partialised(): Reconstruct a matrix from (some of) the parts of a partialised object

dropped_terms(): dropped_terms: Compare terms in full and reduced models

partialise(): partialise: calculate partial components

Dataset/Model/Comparison helpers

Functions that help with handling either the three-layered list corresponding to ‘spec’ descriptions of comparisons, or a simple list of DESeqDataSet objects

compress_dmc(): Generate captioned table

dmc2df(): Convert DMC to dataframe

dmc_heading(): Produce quarto headings corresponding to the data/model hierarchy

Everything Else

Things yet to be categorised

ParamList: R6 class representing the set of parameters used in an analysis

build_dds_list(): Generate subsets of DESeq2 object

check_model(): Check model

compress_dmc(): Generate captioned table

dataset_name(): Wrap dataset-model-comparison object

df2colorspace(): Heatmap colour-scheme generator

dmc2df(): Convert DMC to dataframe

dmc_heading(): Produce quarto headings corresponding to the data/model hierarchy

emcontrasts(): Expand multiple comparisons into their contrasts

export_biologic(): Export Biologic files

fitLRT(): Fit LRT

fit_models(): Fit the DESeq2 models

functional_api(): Orchestrate functional analyses

get_result(): Generate the results for a model and comparison

mult_comp(): Mark a formula as a multiple comparison

plot_tracker(): Generate captioned plot

rbind_summary(): rbind nested lists of data-frames

rebase(): Rebase a factor's level

recode_within(): Recode nested factors

results_apply(): Apply a function to a results list

summarise_results(): Tabulate the size of the differential lists

write_all_results(): Store results as text files

write_assay(): Text file of assay data

write_results(): XLSX report of results

About the package

BABS.RNASeq BABS.RNASeq-package: BABS.RNASeq: BABS RNASeq pipeline