R/get_lipid_absolute_quantification.R
get_lipid_absolute_quantification.Rdget_lipid_absolute_quantification
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") )
| 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 |
Peak plot for each internal standard.
Xiaotao Shen