| import_omics_data | R Documentation |
Import generic omics tsv or csv file
Description
Import generic omics tab- or comma-delimited data file
Usage
import_omics_data(
x,
assay_name = "data",
row_identifier = NULL,
row_annotation_columns = NULL,
curation_txt = NULL,
verbose = FALSE,
...
)
Arguments
x |
one of the following input types:
-
character path to a data file suitable for import
by data.table::fread(), where most delimiters will be recognized
automatically.
-
data.frame representing the equivalent data as from a file.
-
matrix representing only the measured values, with rownames
and colnames that represent respective identifiers.
|
assay_name |
character string which will define the assay name
where data is stored in the resulting SummarizedExperiment object.
|
row_identifier |
defines the column, columns, or rownames, to be
used as row identifiers. These values become rownames(se) for
the output object.
One of the following:
-
NULL (default) which auto-detects an appropriate row identifier:
If the first column is numeric, it uses rownames.
Otherwise the first column is used. If there are duplicated values,
they are made unique with jamba::makeNames().
-
character string of colname in the data x imported.
-
integer column number of data x imported.
The integer value 0 or -1 to indicate rownames(x)
One of these strings, to indicate rownames(x):
"rownames", "rowname", or "row.names".
The default is to use the first column in the imported data x.
|
row_annotation_columns |
defines columns to retain in rowData()
which have non-measurement data associated with each row.
One of the following:
|
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 passed to internal functions
for example data.table::fread().
|
Value
SummarizedExperiment
See Also
Other jam import functions:
coverage_matrix2nmat(),
deepTools_matrix2nmat(),
frequency_matrix2nmat(),
import_lipotype_csv(),
import_metabolomics_niehs(),
import_nanostring_csv(),
import_nanostring_rcc(),
import_nanostring_rlf(),
import_proteomics_PD(),
import_proteomics_mascot(),
import_salmon_quant(),
process_metab_compounds_file()
Examples
x <- matrix(letters[1:9], ncol=3);
rownames(x) <- LETTERS[1:3];
colnames(x) <- letters[1:3];
x
import_omics_data(x)
x <- matrix(1:9, ncol=3);
rownames(x) <- LETTERS[1:3];
colnames(x) <- paste0(letters[1:3], "_rep1");
x
curation_txt <- data.frame(Pattern=LETTERS[1:3], Group="A", Batch="B")
se <- import_omics_data(x, curation_txt=curation_txt)
SummarizedExperiment::assays(se)[[1]]
SummarizedExperiment::colData(se)
SummarizedExperiment::rowData(se)
se2 <- import_omics_data(x, curation_txt=curation_txt[c(2, 1, 3), ])
SummarizedExperiment::assays(se2)[[1]]
SummarizedExperiment::colData(se2)
