annotPSM | R Documentation |
annotPSM
adds fields of annotation to Mascot PSM tables after
rmPSMHeaders
, splitPSM_ma
and cleanupPSM
.
annotPSM(
dat_dir = NULL,
group_psm_by = "pep_seq",
group_pep_by = "prot_acc",
mc_psm_by = "peptide",
fasta = NULL,
expt_smry = "expt_smry.xlsx",
plot_rptr_int = TRUE,
plot_log2FC_cv = TRUE,
rm_allna = FALSE,
type_sd = "log2_R",
engine = "mz",
...
)
dat_dir |
A character string to the working directory. The default is to match the value under the global environment. |
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 |
mc_psm_by |
A character string specifying the method in the median
centering of PSM |
fasta |
Character string(s) to the name(s) of fasta file(s) with
prepended directory path. The |
expt_smry |
A character string to a |
plot_rptr_int |
Logical; if TRUE, the distributions of reporter-ion intensities will be plotted. The default is TRUE. The argument is also applicable to the precursor intensity with MaxQuant LFQ. |
plot_log2FC_cv |
Logical; if TRUE, the distributions of the CV of
peptide |
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 |
engine |
The name of search engine. |
... |
Not currently used. |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.