countInGolden: Counts features from DIA-NN report e.g. Precursor.Id in...

In alzel/proteomicsQC: A set of Routines to plot and analyse DIA-NN reports

Counts features from DIA-NN report e.g. Precursor.Id in golden standard list

Description

Counts features from DIA-NN report e.g. Precursor.Id in golden standard list

Usage

countInGolden(
  report,
  golden_standard,
  feature_var = "Precursor.Id",
  QC_type = "linear_peptides"
)

Arguments

QC_type	comment, default: "linear peptides"
report	DIA-NN report file
golden_standard	golden standard df with feature_var
feature_var	feature variable to count

Examples

LIN_PROTOCOL = "5-min-sswath"
LIN_N = 10
LIN_COR = 0.8
golden_linear = linear_peptides_5minsswath %>% ungroup %>% filter(protocol == LIN_PROTOCOL, n >= LIN_N, cor >= LIN_COR)
countInGolden(report = diann_report,
             golden_standard = golden_linear,
             QC_type = paste(LIN_PROTOCOL, LIN_N, LIN_COR, sep = ":" )) -> golden_linear_counts

alzel/proteomicsQC documentation built on Aug. 11, 2022, 5:58 p.m.