annotatemsbatch {LipidMS}

Lipid annotation for an msbatch

Description

Summarize annotation results of an msbatch into the feature table

Usage

annotatemsbatch(
  msbatch,
  ppm_precursor = 5,
  ppm_products = 10,
  rttol = 5,
  coelCutoff = 0.8,
  lipidClassesPos = c("MG", "LPC", "LPE", "PC", "PCo", "PCp", "PE", "PEo", "PEp", "PG",
    "PI", "Sph", "SphP", "Cer", "CerP", "AcylCer", "SM", "Carnitines", "CE", "DG", "TG"),
  lipidClassesNeg = c("FA", "FAHFA", "LPC", "LPE", "LPG", "LPI", "LPS", "PC", "PCo",
    "PCp", "PE", "PEo", "PEp", "PG", "PI", "PS", "Sph", "SphP", "Cer", "CerP", "AcylCer",
    "SM", "CL", "BA"),
  dbs,
  simplifyAnnotations = FALSE,
  parallel = FALSE,
  ncores
)

Arguments

msbatch

msbatch

ppm_precursor

mass tolerance for precursor ions. By default, 5 ppm.

ppm_products

mass tolerance for product ions. By default, 10 ppm.

rttol

total rt window for coelution between precursor and product ions. By default, 5 seconds.

coelCutoff

coelution score threshold between parent and fragment ions. Only applied if rawData info is supplied. By default, 0.8.

lipidClassesPos

classes of interest in ESI+.

lipidClassesNeg

classes of interest in ESI-.

dbs

list of data bases required for annotation. By default, dbs contains the required data frames based on the default fragmentation rules. If these rules are modified, dbs may need to be supplied. See createLipidDB and assignDB.

simplifyAnnotations

logical. If TRUE, only the most frequent id will be kept (recommended when only pool samples have been acquired in DIA or DDA). If FALSE, all annotations will be shown.

parallel

logical.

ncores

number of cores to be used in case parallel is TRUE.

Value

msbatch

Author(s)

M Isabel Alcoriza-Balaguer <[e-mail]>

Examples

## Not run: 
msbatch <- annotatemsbatch(msbatch)

msbatch$features

## End(Not run)