| import_nanostring_csv | R Documentation |
Import Nanostring csv file
Description
Import Nanostring csv file
Usage
import_nanostring_csv(
csv,
probe_colname = "Probe_ID",
probe_anno_file = NULL,
assay_name = NULL,
hk_count = 10,
curation_txt = NULL,
verbose = FALSE,
...
)
Arguments
csv |
character path to CSV file, suitable for import
by data.table::fread(), so most delimiters will be recognized.
|
probe_colname |
character string used to define the probe
identifier in rowData(), derived from the colnames() of the
import data. Sometimes the values represent "Probe_ID", and
sometimes they may represent "Gene", "miRNA" or another
measurement.
|
probe_anno_file |
character path to one or more files with
additional annotation for each measurement, with identifiers that
match probe_colname above.
|
assay_name |
character string of optional assay name used
in the SummarizedExperiment object created. When NULL the
default is "raw" unless the file contains substring "norm"
in which case it uses "norm".
|
hk_count |
integer number of housekeeper genes to use when
"control_type" is not defined for the imported data.
In this case, the last hk_count genes in the data are
assumed to be housekeeper genes, by typical convention of
NanoString codeset design.
|
curation_txt |
either data.frame or character file path
to tab- or comma-delimited file.
The first column should match the
column headers after importing data, colData(se).
Subsequent columns contain associated sample annotations.
For Nanostring data, the Nanostring sample annotations will already
be associated with the colData(se), and colnames(curation_df)
will overwrite any that already exist.
Pro tip: The first column in curation_txt should contain '.'
instead of punctuation/whitespace, to improve pattern matching
filenames where the punctuation characters may have been modified
during processing.
Note also that when curation_txt is supplied, samples in se
will be subset to include only those samples that match curation_txt,
and in the order they appear in the curation_txt file.
This behavior allows the curation_txt to be used to define
the appropriate experimental ordering, which by default also
defines downstream control factor levels for statistical contrasts.
The first factor level is used as the control value in those
contrasts.
|
verbose |
logical indicating whether to print verbose output.
|
... |
additional arguments are ignored.
|
Value
SummarizedExperiment
See Also
Other jam import functions:
coverage_matrix2nmat(),
deepTools_matrix2nmat(),
frequency_matrix2nmat(),
import_lipotype_csv(),
import_metabolomics_niehs(),
import_nanostring_rcc(),
import_nanostring_rlf(),
import_omics_data(),
import_proteomics_PD(),
import_proteomics_mascot(),
import_salmon_quant(),
process_metab_compounds_file()
