get_lipid_absolute_quantification: get_lipid_absolute_quantification

In jaspershen/lipidflow: What the Package Does (One Line, Title Case)

Description

get_lipid_absolute_quantification

Usage

get_lipid_absolute_quantification(
  path = ".",
  is_info_name_pos = "IS_information.xlsx",
  is_info_name_neg = "IS_information.xlsx",
  use_manual_is_info = FALSE,
  lipid_annotation_table_pos = "lipid_annotation_table_pos.xlsx",
  lipid_annotation_table_neg = "lipid_annotation_table_neg.xlsx",
  chol_rt = 1169,
  output_integrate = TRUE,
  forced_targeted_peak_table_name = NULL,
  fit.gaussian = TRUE,
  integrate_xcms = TRUE,
  output_eic = TRUE,
  ppm = 40,
  rt.tolerance = 180,
  threads = 3,
  rerun = FALSE,
  which_group_for_rt_confirm = "QC",
  match_item_pos = list(Cer = "d18:1 (d7)-15:0 Cer", ChE = c("18:1(d7) Chol Ester",
    "Cholesterol (d7)"), Chol = "Cholesterol (d7)", DG = "15:0-18:1(d7) DAG", LPC =
    "18:1(d7) Lyso PC", LPE = "18:1(d7) Lyso PE", MG = "18:1 (d7) MG", PA =
    "15:0-18:1(d7) PA (Na Salt)", PC = "15:0-18:1(d7) PC", PE = "15:0-18:1(d7) PE", PG =
    "15:0-18:1(d7) PG (Na Salt)", PI = "15:0-18:1(d7) PI (NH4 Salt)", PPE =
    "C18(Plasm)-18:1(d9) PE", PS = "15:0-18:1(d7) PS (Na Salt)", SM =
    "d18:1-18:1(d9) SM", TG = "15:0-18:1(d7)-15:0 TAG"),
  match_item_neg = list(Cer = "d18:1 (d7)-15:0 Cer", Chol = "Cholesterol (d7)", ChE =
    c("18:1(d7) Chol Ester", "Cholesterol (d7)"), LPC = "18:1(d7) Lyso PC", LPE =
    "18:1(d7) Lyso PE", PC = "15:0-18:1(d7) PC", PE = "15:0-18:1(d7) PE", PG =
    "15:0-18:1(d7) PG (Na Salt)", PI = "15:0-18:1(d7) PI (NH4 Salt)", PPE =
    "C18(Plasm)-18:1(d9) PE", PS = "15:0-18:1(d7) PS (Na Salt)", SM =
    "d18:1-18:1(d9) SM")
)

Arguments

path	path.
is_info_name_pos	is_info_name_pos
is_info_name_neg	is_info_name_neg
use_manual_is_info	use_manual_is_info
lipid_annotation_table_pos	lipid_annotation_table_pos
lipid_annotation_table_neg	lipid_annotation_table_neg
chol_rt	chol_rt
output_integrate	output_integrate
forced_targeted_peak_table_name	forced_targeted_peak_table_name
fit.gaussian	fit.gaussian
integrate_xcms	integrate_xcms
output_eic	output_eic
ppm	ppm
rt.tolerance	rt.tolerance
threads	threads
rerun	rerun
which_group_for_rt_confirm	which_group_for_rt_confirm
match_item_pos	match_item_pos
match_item_neg	match_item_neg

Value

Peak plot for each internal standard.

Author(s)

Xiaotao Shen

jaspershen/lipidflow documentation built on March 7, 2021, 2:42 p.m.