Function reference • KRSA

Core Functions

Core functions for the KRSA package

krsa(): Main KRSA function. It performs the random sampling analysis and generates a Z score table and a count matrix

krsa_group_diff(): Calculates LFC based on modeled pw data and grouping

krsa_quick_filter(): Filters out low signal peptides AND none linear peptides

krsa_read(): Read crosstab format files exported from bioNavigator and tidy them

krsa_scaleModel(): Fits, scales, transforms, and normalize kinome array data

Plotting Functions

Functions that generate plots for the KRSA package

krsa_ball_model(): Generates a kinase ball model using the Z score table

krsa_sampling(): Performs random sampling of peptides and mapped kinases

krsa_coverage_plot(): Generates a coverage plot (Percentage of total coverage of kinases on chip)

krsa_curve_plot(): Generates curves plots per peptide using the last cycle data

krsa_heatmap(): Generates a heatmap based on the modeled pw data

krsa_heatmap_grouped(): Generates a grouped heatmap

krsa_histogram_plot(): Generates kinase histogram plots based on the KRSA function output

krsa_reverse_krsa_plot(): Generates the reverse krsa plot (to examine kinase activity)

krsa_violin_plot(): Generates violin plots based on peptides signals intensities

krsa_violin_plot_grouped(): Generates grouped violin plots based on peptides signals intensities with t tests options

krsa_waterfall(): Generates a waterfall figure based on the LFC table

krsa_zscores_plot(): Generates a waterfall figure based on the Z score table

krsa_cv_plot(): Generates CV (coefficient of variation) plot

krsa_ce_output_kinases(): It prepares a KRSA kinase file to be used for creedenzymatic

krsa_ce_output_peptides(): It prepares a KRSA peptide file (log2 FC) to be used for creedenzymatic

parse_BN_crosstabFile(): Parse bionavigator crosstab files

krsa_enrichr_plot(): Visualize the enrichr analysis

Helper Functions

Helper functions for the KRSA package

krsa_extractEndPoint(): Extracts end point data (last cycle)

krsa_extractEndPointMaxExp(): Extracts end point data at max exposure (last cycle)

krsa_get_diff_byChip(): Extract differential peptides based on LFC cutoff by chip/barcode

krsa_get_diff(): Extract differential peptides based on LFC cutoff

krsa_show_peptides(): Determine number of peptides inside lists

krsa_top_hits(): Extracts top kinase hits based on a Z cutoff

krsa_enrichr(): Runs enrichr analysis using a list of PamChip peptide IDs or genes

enrichr_lib_call(): Runs enrichr api (single GET call for a geneset library)

QC Functions

Quality control functions for the KRSA package

krsa_filter_lowPeps(): Filters out peptides with low signals based on the pw data (max exposure)

krsa_filter_nonLinear(): Filters out peptides with none linear signals based on the pw data

krsa_filter_ref_pep(): Filters out ref peptides

krsa_qc_steps(): QC pre-processing of raw data (deals with negative values, and adjust signal saturation values)

Data and curated files

Data and curated files for the KRSA package

KRSA_Mapping_PTK_PamChip_86402_v1: KRSA kinase-substrate mapping file for PamChip 86402 PTK (v1 mapping)

KRSA_Mapping_STK_PamChip_87102_v1: KRSA kinase-substrate mapping file for PamChip 87102 STK (v1 mapping)

KRSA_coverage_PTK_PamChip_86402_v1: KRSA kinase coverage file for PamChip 86402 PTK (v1 mapping)

KRSA_coverage_STK_PamChip_87102_v1: KRSA kinase coverage file for PamChip 87102 STK (v1 mapping)

KRSA_coverage_STK_PamChip_87102_v2: KRSA kinase coverage file for PamChip 87102 STK (v2 mapping, removed PDK kinase)

ballModel_edges: Protein-Protein Interactions based on PhosphositePlus database

ballModel_nodes: Protein-Protein Interactions based on PhosphositePlus database

stk_pamchip_87102_mapping: CDRL Complete mapping of peptides to HGNC symbols (STK PamChip 87102)

ptk_pamchip_86402_mapping: CDRL Complete mapping of peptides to HGNC symbols (PTK PamChip 86402)