Function reference • KRSA

Core Functions
`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
`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
`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
`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
`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)

Reference

Core Functions

Plotting Functions

Helper Functions

QC Functions

Data and curated files