normPep_Mplex | R Documentation |
Median summary of data from the same TMT or LFQ experiment at different LCMS
injections summed pep_n_psm
, prot_n_psm
, and prot_n_pep
after data merging no Z_log2_R yet available use col_select =
expr(Sample_ID)
not col_select
to get all Z_log2_R why: users may
specify col_select
only partial to Sample_ID entries.
normPep_Mplex(
group_psm_by = "pep_seq_mod",
group_pep_by = "prot_acc",
use_duppeps = TRUE,
duppeps_repair = "denovo",
cut_points = Inf,
omit_single_lfq = FALSE,
use_mq_pep = FALSE,
rm_allna = FALSE,
ret_sd_tol = Inf,
rm_ret_outliers = FALSE,
...
)
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 |
use_duppeps |
Logical; if TRUE, re-assigns double/multiple dipping peptide sequences to the most likely proteins by majority votes. |
duppeps_repair |
Not currently used (or only with For instance, the same sequence of PEPTIDE may be assigned to protein
accession PROT_ACC1 in data set 1 and PROT_ACC2 in data set 2. At the
|
cut_points |
A named, numeric vector defines the cut points (knots) for
the median-centering of |
omit_single_lfq |
Logical; if TRUE, omits LFQ entries with single measured values across all samples. The default is FALSE. |
use_mq_pep |
Logical; if TRUE, uses the peptides.txt from MaxQuant. This is an interim solution for MaxQuant timsTOF. |
rm_allna |
Logical; if TRUE, removes data rows that are exclusively NA
across ratio columns of |
ret_sd_tol |
Numeric; the tolerance in the variance of retention time
(w.r.t. measures in seconds). The thresholding applies to both TMT and LFQ
data. The default is |
rm_ret_outliers |
Logical; if TRUE, removes peptide entries with outlying retention times across samples and/or LCMS series. |
... |
|
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