readSCP {scp} | R Documentation |
Read single-cell proteomics data as a QFeatures object from
tabular data and metadata
Description
Convert tabular quantitative MS data and metadata from a
spreadsheet or a data.frame
into a QFeatures object containing
SingleCellExperiment objects.
Usage
readSCP(
featureData,
colData,
batchCol,
channelCol,
suffix = NULL,
removeEmptyCols = FALSE,
verbose = TRUE,
...
)
Arguments
featureData |
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.
|
colData |
A data.frame or any object that can be coerced
to a data.frame . colData is expected to contains all the
sample meta information. Required fields are the acquisition
batch (given by batchCol ) and the acquisition channel within
the batch (e.g. TMT channel, given by
channelCol ). Additional fields (e.g. sample type,
acquisition date,...) are allowed and will be stored as sample
meta data.
|
batchCol |
A numeric(1) or character(1) pointing to the
column of featureData and colData that contain the batch
names. Make sure that the column name in both table are either
identical and syntactically valid (if you supply a character )
or have the same index (if you supply a numeric ). Note that
characters can be converted to syntactically valid names using
make.names
|
channelCol |
A numeric(1) or character(1) pointing to the
column of colData that contains the column names of the
quantitative data in featureData (see Example).
|
suffix |
A character() giving the suffix of the column
names in each assay. The length of the vector should equal the
number of quantification channels and should contain unique
character elements. If NULL, the names of the quantification
columns in featureData are taken as suffix.
|
removeEmptyCols |
A logical(1) . If true, the function will
remove in each batch the columns that contain only missing
values.
|
verbose |
A logical(1) indicating whether the progress of
the data reading and formatting should be printed to the
console. Default is TRUE .
|
... |
Further arguments that can be passed on to read.csv
except stringsAsFactors , which is always FALSE .
|
Value
An instance of class QFeatures. The expression data of
each batch is stored in a separate assay as a
SingleCellExperiment object.
Note
The SingleCellExperiment
class is built on top of the
RangedSummarizedExperiment
class. This means that some column names
are forbidden in the rowData
. Avoid using the following names:
seqnames
, ranges
, strand
, start
, end
,
width
, element
Author(s)
Laurent Gatto, Christophe Vanderaa
Examples
## Load an example table containing MaxQuant output
data("mqScpData")
## Load the (user-generated) annotation table
data("sampleAnnotation")
## Format the tables into a QFeatures object
readSCP(featureData = mqScpData,
colData = sampleAnnotation,
batchCol = "Raw.file",
channelCol = "Channel")
[Package
scp version 1.3.3
Index]