convert_PD_df_to_SE: Internal function to convert Proteomics Discoverer data.frame...

In jmw86069/platjam: Platform Jam, biological platform importers.

Internal function to convert Proteomics Discoverer data.frame to SummarizedExperiment

Description

Internal function to convert Proteomics Discoverer data.frame to SummarizedExperiment

Usage

convert_PD_df_to_SE(
  protein_df,
  ann_lib = c("org.Hs.eg.db"),
  curation_txt = NULL,
  ptm_colname = "Modifications",
  type = c("protein", "peptide"),
  remove_duplicate_peptides = TRUE,
  accession_from = NULL,
  accession_to = NULL,
  xref_df = NULL,
  verbose = FALSE,
  ...
)

Details

This function is intended to be called by import_proteomics_PD() after the Excel data is split into protein and peptide data.frame components.

See Also

Other jam utility functions: cardinality(), color_complement(), convert_imputed_assays_to_na(), curate_se_colData(), curate_to_df_by_pattern(), design2layout(), get_numeric_transform(), handle_df_args(), merge_proteomics_se(), nmat_summary(), nmatlist_summary(), rmd_tab_iterator(), rowNormScale(), summit_from_vector()

jmw86069/platjam documentation built on Sept. 26, 2024, 3:31 p.m.