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Get EICs from xcmsRaw object

Source: R/get_EIC.R
get_EICs.Rd

Takes an xcmsRaw object and extracts EICs. Can do multiple ranges and exclude certain masses unlike getEIC. Can be used to extract the TIC too.

Usage

get_EICs(
  xraw,
  range_tbl,
  exclude_mz = NULL,
  exclude_ppm = 30,
  range_tbl_cols = c("mz_lower", "mz_upper"),
  BPI = FALSE,
  min_int = 0
)

Arguments

xraw

xcmsRaw object to get EIC(s)/TIC from.

range_tbl

data.frame/tibble with columns for the lower and upper m/z boundaries of EIC slice(s).

exclude_mz

Masses to exclude from the EIC. Most useful to remove contaminants from TICs.

exclude_ppm

ppm tolerance of exclude_mz

range_tbl_cols

Which columns in range_tbl holds the lower and upper range. defaults to c("mz_lower","mz_upper").

BPI

Logical selecting to calculate TIC (FALSE) or BPI.

min_int

the minimum intensity mass peak to include

Value

tbl A tibble containing the columns:

  • scan: scan number

  • scan_rt: Retention time of scan

  • intensity: The summed intensity for each scan in the given m/z interval