Description Usage Arguments Details Value Examples
View source: R/evidenceToSAINTqFormat.R
Converts the MaxQuant evidence file to the required files
by SAINTq. The user can choose to use either peptides with spectral counts
(use msspc
) or the all the peptides (use all
) for the analysis.
The quantitative can be also chosen (either MS Intensity or Spectral Counts)
1 2 3 4 5 6 7 8 9 | artmsEvidenceToSAINTq(
evidence_file,
keys_file,
output_dir = "artms_saintq",
sc_option = c("all", "msspc"),
fractions = FALSE,
quant_variable = c("msint", "msspc"),
verbose = TRUE
)
|
evidence_file |
(char or data.frame) The evidence file path and name, or data.frame |
keys_file |
(char) Keys file with a SAINT column specifying
test ( |
output_dir |
(char) New directory to create and save files. Default is current directory (recommended to provide a new folder name). |
sc_option |
(char). Filter peptides with spectral counts only. Two options:
|
fractions |
(logical) |
quant_variable |
(char) Select the quantitative variable. Two options available:
|
verbose |
(logical) |
After running the script, the new specified folder should contain the folling files:
saintq-config-peptides
saintq-config-proteins
saintq_input_peptides.txt
saintq_input_proteins.txt
Then cd
into the new folder and run either of the following two options
(assuming that saintq
is installed in your linux/unix/mac os x system):
> saintq config-saintq-peptides
or
> saintq config-saintq-proteins
The input files requires to run SAINTq
1 2 3 4 |
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