View source: R/createQCreportObject.R
Create initial qcrepotobject structure from input variable
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | createQCreportObject(
data_file,
projectdir,
author = "",
metaData_file = NULL,
raw_path = NULL,
InternalProjectRef = "",
Dataset = "",
Organisation = "",
QC_label = "QC",
Blank_label = "Blank",
classLabel = "Class",
excludeQC = c(1L:5L),
assay = NULL,
plot_eic = TRUE,
pca_scores_labels = "all",
mv_filter_method = "across",
mv_filter_frac = 0.5,
xcms_output = "xset",
msms_label = "MSMS",
group_names = NULL
)
|
data_file |
Rdata file containing XCMS output, object should be called xset |
projectdir |
Folder where Rdata file is located and where output should be directed |
author |
Character sring woth reports author name, optional |
metaData_file |
Files in xlsx format containing sample names and class labels |
raw_path |
File path where mzML files are located |
InternalProjectRef |
Character string containing project reference, optional |
Dataset |
Character string to describe data set, optional |
Organisation |
Character string containing organisation name, optional |
QC_label |
Label used for QC samples |
Blank_label |
Label usef for QC samples |
classLabel |
Columns name in meta data file to use for class labels, default value is Class |
excludeQC |
Which QC samples to exclude from RSD% calculations, signal batch correction and PCA plots |
assay |
Names for analytical assay, if set to NULL name of the input Rdata file will be used |
plot_eic |
Will create pdf fail with selected peak EIC's if set to TRUE |
pca_scores_labels |
Defines if sample labels should be added to filtered data PCA scores plot |
mv_filter_method |
Defines what method for MV filter |
mv_filter_frac |
Threshod of faction of detection of MV filter |
xcms_output |
Name of the R object in Rdata file containing XCMS outputs |
msms_label |
Label used for MS/MS data files |
group_names |
character(), character vector containing uique sample group identifiers in the raw data files. If left empty function will attemp to fill in class labels for blank and QC samples. |
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