plotGoldenCounts: Plots combined DIA-NN experiment with Golden standarts...
In alzel/proteomicsQC: A set of Routines to plot and analyse DIA-NN reports

plotGoldenCounts

R Documentation

Plots combined DIA-NN experiment with Golden standarts metrics

Description

Plots combined DIA-NN experiment with Golden standarts metrics

Usage

plotGoldenCounts(
  data_counts,
  metadata,
  golden_thr = 0.9,
  qc_pattern = ".*?QC.*?"
)

Arguments

`metadata`	experiment description to arrange by run_order output from `create_metadata`
`golden_thr`	threshold for QC line, default = 0.8
`qc_pattern`	QC file pattern
`data_counts`	output from `countInGolden`

Value

list of plot and samples bellow golden_thr

Examples

LIN_PROTOCOL <- "5-min-sswath"
LIN_N <- 10
LIN_COR <- 0.8
LIN_PROTOCOL = "5-min-sswath"
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

metadata <- create_metadata(diann_report)
ret = plotGoldenCounts(golden_linear_counts, metadata, golden_thr = 0.1)

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