PStoMSstatsPTMFormat | R Documentation |
Currently only supports label-free quantification.
PStoMSstatsPTMFormat(
input,
annotation,
input_protein = NULL,
annotation_protein = NULL,
use_unmod_peptides = FALSE,
target_modification = NULL,
remove_oxidation_peptides = FALSE,
remove_multi_mod_types = FALSE,
summaryforMultipleRows = max,
use_log_file = TRUE,
append = FALSE,
verbose = TRUE,
log_file_path = NULL
)
input |
name of Peaks Studio PTM output |
annotation |
name of annotation file which includes Raw.file, Condition, BioReplicate, Run. For example annotation see example below. |
input_protein |
name of Peaks Studio unmodified protein output (optional) |
annotation_protein |
name of annotation file which includes Raw.file, Condition, BioReplicate, Run for unmodified protein output. |
use_unmod_peptides |
Boolean if the unmodified peptides in the input
file should be used to construct the unmodified protein output. Only used if
|
target_modification |
Character name of modification of interest. To
use all mod types, leave as |
remove_oxidation_peptides |
Boolean if Oxidation (M) modifications
should be removed. Default is |
remove_multi_mod_types |
Used if |
summaryforMultipleRows |
max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities. |
use_log_file |
logical. If TRUE, information about data processing will be saved to a file. |
append |
logical. If TRUE, information about data processing will be added to an existing log file. |
verbose |
logical. If TRUE, information about data processing wil be printed to the console. |
log_file_path |
character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If 'append = TRUE', has to be a valid path to a file. |
list
of data.table
# The output should be in the following format.
head(raw.input$PTM)
head(raw.input$PROTEIN)
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