process_similarity: Searching a query spectrum in a spectral library The function...

In daniellyz/MergeION2: Merging and Networking Scans from Multiple LC-MS/MS Raw Data Files

Searching a query spectrum in a spectral library The function calculates spectral similarity of a query spectrum to an existing spectral library

Description

Searching a query spectrum in a spectral library The function calculates spectral similarity of a query spectrum to an existing spectral library

Usage

process_similarity(
  query_spectrum,
  polarity = "Positive",
  prec_mz = 100,
  use.loss = TRUE,
  use.prec = FALSE,
  input_library = NULL,
  method = c("Precision", "Recall", "F1", "Cosine", "Spearman", "MassBank", "NIST", "HM",
    "Entropy"),
  prec_ppm_search = 10,
  frag_mz_search = 0.005,
  min_frag_match = 6
)

Arguments

query_spectrum	two columns spectrum list
use.loss	boolean if natrual loss also be used, prec_mz can not be missing if set true.
input_library	Character or a list object. If character, file name with extension mgf, msp or RData. If list, must contain "complete", "consensus" and "network".

Author(s)

Youzhong Liu, [e-mail]

daniellyz/MergeION2 documentation built on Feb. 12, 2025, 11:23 a.m.