Convert tabular data from a spreadsheet or a data.frame into a
QFeatures object.
readQFeatures(table, ecol, fnames, ..., name = NULL)
readSummarizedExperiment(table, ecol, fnames, ...)File or object holding the quantitative data. Can be
either a character(1) with the path to a text-based
spreadsheet (comma-separated values by default, but see ...)
or an object that can be coerced to a data.frame. It is
advised not to encode characters as factors.
A numeric indicating the indices of the columns to
be used as expression values. Can also be a character
indicating the names of the columns. Caution must be taken if
the column names are composed of special characters like (
or - that will be converted to a . by the read.csv
function. If ecol does not match, the error message will
display the column names as seen by the read.csv function.
An optional character(1) or numeric(1)
indicating the column to be used as feature names.
Further arguments that can be passed on to read.csv
except stringsAsFactors, which is always FALSE.
An character(1) to name assay in the QFeatures
object. If not set, features is used.
An instance of class QFeatures or SummarizedExperiment.
readQFeatures: See description.
readSummarizedExperiment: Convert tabular data from a spreadsheet or a
data.frame into a SummarizedExperiment object.
The QFeatures class for an example on how to use
readQFeatures and how to further manipulate the resulting data.
## Load a data.frame with PSM-level data
data(hlpsms)
## Create the QFeatures object
fts2 <- readQFeatures(hlpsms, ecol = 1:10, name = "psms")
fts2
#> An instance of class QFeatures containing 1 assays:
#> [1] psms: SummarizedExperiment with 3010 rows and 10 columns