psm_to_pep | R Documentation |
Helper of PSM2Pep
psm_to_pep(
file = NULL,
df = NULL,
dat_dir = NULL,
label_scheme_full = NULL,
group_psm_by = "pep_seq",
group_pep_by = "prot_acc",
method_psm_pep = "median",
lfq_ret_tol = 60L,
rm_allna = FALSE,
type_sd = "log2_R",
engine = "mz",
lfq_mbr = FALSE,
trace_files = NULL,
...
)
file |
The name of a PSM file. |
df |
A PSM table. |
dat_dir |
A character string to the working directory. The default is to match the value under the global environment. |
label_scheme_full |
The label_scheme with the probable inclusion of different LCMS_inj under the same TMT_Set. |
group_psm_by |
A character string specifying the method in PSM grouping.
At the |
group_pep_by |
A character string specifying the method in peptide
grouping. At the |
method_psm_pep |
Character string; the method to summarize the
|
lfq_ret_tol |
The tolerance of retention time (in seconds) for the aggregation of LFQ data. |
rm_allna |
Logical; if TRUE, removes data rows that are exclusively NA
across ratio columns of |
type_sd |
Character string; the type of log2Ratios for SD calculations.
The value is one |
lfq_mbr |
Logical; performs MBR for LFQ or not. |
... |
filter_dots. |
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