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Summary report

get_summary_Report.Rd

Generates a summary report

Usage

get_summary_Report(
  input_list,
  CV_RT_th_hold = 5,
  CV_LFQ_Pep_th_hold = 20,
  CV_LFQ_PG_th_hold = 20
)

Arguments

input_list

A list with data frames including ID, DC, MC, LFQ and RT information.

CV_RT_th_hold

Numeric. User-specified threshold for CV value of retention time precision. Default is 5.

CV_LFQ_Pep_th_hold

Numeric. User-specified threshold for CV value of quantitative precision. Default is 20.

CV_LFQ_PG_th_hold

Numeric. User-specified threshold for CV value of quantitative precision. Default is 20.

Value

This function returns a list. For each analysis a respective data frame is stored in the list with the following information:

  • Analysis - analysis name.

  • "Median ProteinGroup.IDs abs." - median number of proteingroup identifications.

  • "Median Protein.IDs abs." - median number of protein identifications.

  • "Median Peptide.IDs abs." - median number of peptide identifications.

  • "Median Precursor.IDs abs." - median number of precursor identifications.

  • "Full profile - Precursor.IDs abs." - number of precursor identifications for full profiles.

  • "Full profile - Peptide.IDs abs." - number of peptide identifications for full profiles.

  • "Full profile - Protein.IDs abs." - number of protein identifications for full profiles.

  • "Full profile - ProteinGroup.IDs abs." - number of proteingroup identifications for full profiles.

  • "Full profile - Precursor.IDs %" - number of precursor identifications for full profiles in percentage.

  • "Full profile - Peptide.IDs %" - number of peptide identifications for full profiles in percentage.

  • "Full profile - Protein.IDs %" - number of protein identifications for full profiles in percentage.

  • "Full profile - ProteinGroup.IDs %" - number of proteinGroup identifications for full profiles in percentage.

  • "Precursor.IDs abs. with a CV Retention time < X %" - number of precursor identifications with a CV value for retention time precision under user-specified threshold X.

  • "Proteingroup.IDs abs. with a CV LFQ < X %" - number of proteingroup identifications with a CV value for quantitative precision under user-specified threshold X.

  • "Peptide.IDs abs. with a CV LFQ < X %" - number of peptide identifications with a CV value for quantitative precision under user-specified threshold X.

  • "Peptide IDs with zero missed cleavages abs." - number of peptide identifications with zero missed cleavages.

  • "Peptide IDs with zero missed cleavages %" - number of peptide identifications with zero missed cleavages in percentage.

Details

For each submitted data a summary report including information about achieved identifications (ID), data completeness (DC), missed cleavages (MC), and both quantitative (LFQ) and retention time (RT) precision is generated.

Author

Oliver Kardell

Examples

# Load libraries
library(tibble)

# Example data
data <- list(
DIANN = list(
 filename = "B",
 software = "DIA-NN",
 data = list(
   "DIA-NN" = tibble::tibble(
     "Run_mpwR" = c("R01", "R01", "R02", "R03", "R01"),
     "Precursor.IDs_mpwR" = c("A1", "A1", "A1", "A1", "B2"),
     "Retention.time_mpwR" = c(3, 3.5, 4, 5, 4),
     "ProteinGroup_LFQ_mpwR" = c(3, 4, 5, 4, 4),
     "Peptide.IDs_mpwR" = c("A", "A", "A", "A", "B"),
     "Protein.IDs_mpwR" = c("A", "A", "A", "A", "B"),
     "ProteinGroup.IDs_mpwR" = c("A", "A", "A", "A", "B"),
     "Stripped.Sequence_mpwR" = c("ABCR", "AKCR", "ABKCK", "ARKAR", "ABCDR")
   )
 )
)
)

# Result
output <- get_summary_Report(
  input_list = data
)