Package index • proteoDeconv

Data preprocessing

Functions for handling and processing protein data.

handle_duplicates(): Handle duplicate identifiers in an expression matrix

extract_identifiers(): Extract primary identifiers from e.g. protein groups

update_gene_symbols(): Update gene symbols in a matrix to approved HGNC nomenclature

unlog2_data(): Convert data from log2 scale to linear scale

convert_to_tpm(): Convert protein abundance data to TPM-like normalization

handle_scaling(): Handle scaling of protein abundance data

handle_missing_values(): Handle missing values

Signature matrix creation

Functions for working with signature matrix creation.

map_cell_groups(): Map column names to cell type groups using patterns

create_phenoclasses(): Create phenoclasses matrix for cell type deconvolution

create_signature_matrix(): Create signature matrix using CIBERSORTx

Deconvolution

Functions for deconvoluting bulk data into cell type proportions.

deconvolute(): Deconvolute protein data using multiple algorithms

deconvolute_bayesdebulk(): Deconvolute bulk proteome data using BayesDeBulk

deconvolute_cibersort(): Deconvolute mixture data using CIBERSORT

deconvolute_cibersortx(): Deconvolute using CIBERSORTx Docker image

deconvolute_epic(): Deconvolute bulk data using EPIC

Simulation

Function for simulating artifical mixtures.

simulate_data(): Simulate artifical mixtures from bulk proteome measurements