Reads NULISAseq XML file
readNULISAseq(
file,
plateID = NULL,
file_type = "xml_no_mismatches",
target_column_names = NULL,
sample_column_names = NULL,
sample_group_covar = NULL,
IC = NULL,
IPC = NULL,
SC = NULL,
NC = NULL,
Calibrator = NULL,
replaceNA = TRUE,
allowMissingCurveQuant = FALSE,
canonicalTargets = TRUE,
targetMap = NULL
)Character string. Path and name of the file.
Character string that denotes plate ID.
Character string. Type of input file.
Options include xml_no_mismatches, xlsx (output from ACC)
or csv_long (output from writeNULISAseq() function).
A vector of column names for target-specific data
that will appear in the target data frame output.
Only used for csv_long format, and only needed when target column names
are different from the default, which are c('Target', 'AlamarTargetID',
'UniProtID', 'ProteinName').
A vector of column names for sample-specific data
that will appear in the sample data frame output.
Only used for csv_long format, and only needed when sample column names
are different from the default. Default includes all column names in the csv except
for the target column names, given above (either the default or whatever is specified),
and the following: c('Panel', 'PanelLotNumber', 'LOD', 'NPQ').
The sample-specific data
will include by default c('PlateID', 'SampleName', 'SampleType', 'SampleQC').
In addition, by default, it will include any other variables in the dataset.
If sample_column_names is specified, however, it will only include
those variables in the sample data frame output.
string that represents the name of the covariate that defines sample group information. Defaults to NULL. Typically, this covariate defines whether each sample is plasma, serum, csf, etc. This information can be used when reporting detectability. For instance report sample group specific detectability values, etc.).
string(s) that represents the names of internal control targets.
Default is 'mCherry'.Only used for xml file formats.
string(s) present in the sample names
that represent the inter-plate control wells.
For example, 'IPC'. Set to NULL (default) to use the
type variable from the Barcode B file or if there are no IPCs.
Only used for xml file formats.
string(s) present in the sample names
that represent the sample control wells.
For example, 'SC'. Set to NULL (default) to use the
type variable from the Barcode B file or if there are no IPCs.
Only used for xml file formats.
string(s) present in the sample names
that represent the negative control wells.
For example, 'NC'. Set to NULL (default) to use the
type variable from the Barcode B file or if there are no NCs.
Only used for xml file formats.
string(s) present in the sample names
that represent the calibrator wells.
Set to NULL (default) to use the
type variable from the Barcode B file or
if there are no calibrator samples (default).
Only used for xml file formats.
Logical. If TRUE (default), will replace missing counts with zeros.
Logical. If FALSE (default), an error is raised when the XML file contains no Curve_Quant values. Set to TRUE to fall back to treating all targets as forward curve with a warning.
Logical. If TRUE (default), each parsed
targetName is rewritten to the canonical spelling
alamar_target_map lists for its AlamarTargetID, before
any matrix is keyed by targetName. A row with no id is backfilled
from the table (current or alias spelling). A spelling the table lists
under several ids, on a row with no id, takes the id whose table
species matches the plate's species (from Assay: a panel
named for a species is that species, another named panel is Human; for
an absent or generic NULISAseq assay the species is guessed from
the ids already resolved on the plate). When no single id
remains, the row keeps its parsed spelling, AlamarTargetID stays
NA, and a warning names the file and every candidate id. The
as-parsed spelling is kept in
targets$targetName_raw. IC and excludeTargets accept
either the canonical spelling or the spelling parsed from this file; IC
names are matched exactly. Set to FALSE to keep names exactly as
parsed; targetName_raw is then omitted and AlamarTargetID is
left as parsed (NA_character_ when the XML carries none).
Only used for xml file formats.
NULL (default), or user-supplied
targetName -> alamarTargetID aliases layered on top of the shipped
table for this one read. Same shape as insertAlamarTargetIDXML(targetMap = ):
a data.frame or CSV path with exactly one targetName column and one
alamarTargetID column (case-insensitive headers). Every id must
already be a row of alamar_target_map; a name the table
already lists under several ids may be disambiguated this way. Ignored for
a row that already carries an id, and ignored entirely when
canonicalTargets = FALSE.
Only used for xml file formats.
List of lists, data frames, and matrices. Output will differ slightly depending on the input file type.