qc_peak_width: Peak width over retention time

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Peak width over retention time

Description

Plots one minute binned median precursor elution peak width over retention time for each sample.

Usage

qc_peak_width(
  data,
  sample,
  intensity,
  retention_time,
  peak_width = NULL,
  retention_time_start = NULL,
  retention_time_end = NULL,
  remove_na_intensities = TRUE,
  interactive = FALSE
)

Arguments

data	a data frame containing at least sample names and protein IDs.
sample	a character column in the data data frame that contains the sample names.
intensity	a numeric column in the data data frame that contains intensities. If remove_na_intensities = FALSE, this argument is not required.
retention_time	a numeric column in the data data frame that contains retention times of precursors.
peak_width	a numeric column in the data data frame that contains peak width information. It is not required if retention_time_start and retention_time_end columns are provided.
retention_time_start	a numeric column in the data data frame that contains the start time of the precursor elution peak. It is not required if the peak_width column is provided.
retention_time_end	a numeric column in the data data frame that contains the end time of the precursor elution peak. It is not required if the peak_width column is provided.
remove_na_intensities	a logical value that specifies if sample/grouping combinations with intensities that are NA (not quantified IDs) should be dropped from the data frame. Default is TRUE since we are usually interested in the peak width of quantifiable data.
interactive	a logical value that specifies whether the plot should be interactive (default is FALSE).

Value

A line plot displaying one minute binned median precursor elution peak width over retention time for each sample.

Examples

data <- data.frame(
  r_file_name = c(rep("sample_1", 10), rep("sample2", 10)),
  fg_quantity = c(rep(2000, 20)),
  eg_mean_apex_rt = c(rep(c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10), 2)),
  eg_start_rt = c(0.5, 1, 3, 4, 5, 6, 7, 7.5, 8, 9, 1, 2, 2, 3, 4, 5, 5, 8, 9, 9),
  eg_end_rt = c(
    1.5, 2, 3.1, 4.5, 5.8, 6.6, 8, 8, 8.4,
    9.1, 3, 2.2, 4, 3.4, 4.5, 5.5, 5.6, 8.3, 10, 12
  )
)
qc_peak_width(
  data,
  sample = r_file_name,
  intensity = fg_quantity,
  retention_time = eg_mean_apex_rt,
  retention_time_start = eg_start_rt,
  retention_time_end = eg_end_rt
)

protti documentation built on Oct. 22, 2024, 1:06 a.m.