Reference

All functions

annotate()

Annotate positions based on the deep mutational landscape

as_tibble(<deep_mutational_scan>) as.data.frame(<deep_mutational_scan>) as.list(<deep_mutational_scan>)

Convert deep_mutational_scan objects

bind_scans()

Combine deep mutational scan data

check_data()

Check a deep_mutational_scan for common anomalies

cosine_distance_matrix()

Cosine distance matrix

deep_landscape

Deep Mutational Landscape data from 28 standardised deep mutational scans

deep_mutational_scan()

Deep mutational scan data

deep_scans

Example deep_mutational_scan objects

deepscanscape

deepscanscape: Check and Annotate Deep Mutational Scanning Data

describe_clusters()

Describe amino acid positional subtypes

`[`(<deep_mutational_scan>) `[<-`(<deep_mutational_scan>)

Extracting and replacing deep mutational scanning data

autoplot(<deep_mutational_scan>) plot(<deep_mutational_scan>)

Summary plot for Deep Mutational Scans

format(<deep_mutational_scan>) print(<deep_mutational_scan>) str(<deep_mutational_scan>) dim(<deep_mutational_scan>)

General S3 Methods for Deep Mutational Scans

summary(<deep_mutational_scan>) format(<deep_mutational_scan_summary>) print(<deep_mutational_scan_summary>)

Summarise Deep Mutational Scans

generate_report()

Generate an HTML report for new deep mutational scan data

impute()

Impute missing deep mutational scan data

is.deep_mutational_scan()

Determine if an object is a deep_mutational_scan

landscape_outliers()

Identify positions outside the mutational landscape

new_deep_mutational_scan()

Internal deep_mutational_scan constructor

normalise_er()

Normalise deep mutational scanning fitness scores

parse_deep_scan()

Parse deep mutational scanning data

parse_mavedb()

Parse data in the MaveDB format

parse_sequence()

Parse data in the sequence format

parse_wide()

Parse data in the wide format

plot_cluster_frequencies()

Plot amino acid subtype frequencies

plot_er_distribution()

Plot ER distributions

plot_er_heatmap()

Plot a heat map of ER scores from a deep mutational scan

plot_landscape()

Plot a new study on the deep mutational landscape

plot_recluster()

Summarise a deep mutational scan recluster

recluster()

Recluster DMS data with a combined dataset

subtypes

Amino acid positional subtypes from the deep mutational landscape

theme_deepscanscape()

Default deepscanscape GGPlot2 theme

transform_er()

Transform deep_mutational scanning scores onto a standard scale

transform_vamp()

Transform VAMP-Seq fitness scores

validate_deep_mutational_scan()

Validate deep_mutational_scan objects