SkylinetoMSstatsPTMFormat | R Documentation |
Currently only supports label-free quantification.
SkylinetoMSstatsPTMFormat(
input,
fasta_path,
fasta_protein_name = "uniprot_iso",
annotation = NULL,
input_protein = NULL,
annotation_protein = NULL,
use_unmod_peptides = FALSE,
removeiRT = TRUE,
filter_with_Qvalue = TRUE,
qvalue_cutoff = 0.01,
use_unique_peptide = TRUE,
remove_few_measurements = FALSE,
remove_oxidation_peptides = FALSE,
removeProtein_with1Feature = FALSE,
use_log_file = TRUE,
append = FALSE,
verbose = TRUE,
log_file_path = NULL
)
input |
name of Skyline PTM output |
fasta_path |
A string of path to a FASTA file, used to match PTM peptides. |
fasta_protein_name |
Name of fasta column that matches with protein name
in evidence file. Default is |
annotation |
name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Skyline, use annotation=NULL (default). It will use the annotation information from input. |
input_protein |
name of Skyline unmodified protein output (optional) |
annotation_protein |
name of 'annotation.txt' data which includes Condition,
BioReplicate, Run for unmodified protein output. This can be the same as
|
use_unmod_peptides |
Boolean if the unmodified peptides in the input
file should be used to construct the unmodified protein output. Only used if
|
removeiRT |
TRUE (default) will remove the proteins or peptides which are labeld 'iRT' in 'StandardType' column. FALSE will keep them. |
filter_with_Qvalue |
TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in DetectionQValue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose. |
qvalue_cutoff |
Cutoff for DetectionQValue. default is 0.01. |
use_unique_peptide |
TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein. |
remove_few_measurements |
TRUE will remove the features that have 1 or 2 measurements across runs. FALSE is default. |
remove_oxidation_peptides |
TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default. |
removeProtein_with1Feature |
TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default. |
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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