filter_TMT_PSMs: Filter a PSM-level MSnSet to remove low quality PSMs

In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data

Filter a PSM-level MSnSet to remove low quality PSMs

Description

Filter PSMs from TMT quantification to remove the following:

1. Missing values (NA) for all tags

2. Interference/co-isolation above a set value (default=100, e.g no filtering)

3. Signal:noise ratio below a set value (default=0, e.g no filtering)

Filter PSMs from TMT quantification to remove the following

1. Missing values (NA) for all tags

2. Interference/co-isolation above a set value (default=100, e.g no filtering)

3. Signal:noise ratio below a set value (default=0, e.g no filtering)

Usage

filter_TMT_PSMs(
  obj,
  inter_thresh = 100,
  sn_thresh = 0,
  master_protein_col = "Master.Protein.Accessions",
  inter_col = "Isolation.Interference.in.Percent",
  sn_col = "Average.Reporter.SN",
  verbose = TRUE
)

filter_TMT_PSMs(
  obj,
  inter_thresh = 100,
  sn_thresh = 0,
  master_protein_col = "Master.Protein.Accessions",
  inter_col = "Isolation.Interference.in.Percent",
  sn_col = "Average.Reporter.SN",
  verbose = TRUE
)

Arguments

obj	MSnSet PSMs
inter_thresh	numeric Maximum allowed interference/co-isolation
sn_thresh	numeric Minimum allowed signal:noise threshold
master_protein_col	string. Name of column containing master proteins.
inter_col	string Name of column containing the interference value
sn_col	string Name of column containing the signal:noise value
verbose	boolean. Default is TRUE, use verbose output messages.

Value

Returns an MSnSet with the filtered PSMs.

MSnSet with the filtered PSMs.

CambridgeCentreForProteomics/camprotR documentation built on July 7, 2024, 2:13 a.m.