Description Usage Arguments Value Author(s) Examples
The compData
class is used to store information about the experiment, such as the count matrix, sample and variable annotations, information regarding the generation of the data and results from applying a differential expression analysis to the data. This constructor function creates a compData
object.
1 2 3 4 5 6 7 8 9 10 11 12 | compData(
count.matrix,
sample.annotations,
info.parameters,
variable.annotations = data.frame(),
filtering = "no info",
analysis.date = "",
package.version = "",
method.names = list(),
code = "",
result.table = data.frame()
)
|
count.matrix |
A count matrix, with genes as rows and observations as columns. |
sample.annotations |
A data frame, containing at least one column named 'condition', encoding the grouping of the observations into two groups. The row names should be the same as the column names of the |
info.parameters |
A list containing information regarding simulation parameters etc. The only mandatory entries are
|
variable.annotations |
A data frame with variable annotations (with number of rows equal to the number of rows in
|
filtering |
A character string containing information about the filtering that has been applied to the data set. |
analysis.date |
If a differential expression analysis has been performed, a character string detailing when it was performed. |
package.version |
If a differential expression analysis has been performed, a character string giving the version of the differential expression packages that were applied. |
method.names |
If a differential expression analysis has been performed, a list with entries |
code |
If a differential expression analysis has been performed, a character string containing the code that was run to perform the analysis. The code should be in R markdown format, and can be written to an HTML file using the |
result.table |
If a differential expression analysis has been performed, a data frame containing the results of the analysis. The number of rows should be equal to the number of rows in
|
A compData
object.
Charlotte Soneson
1 2 3 4 |
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Registered S3 method overwritten by 'gplots':
method from
reorder.factor gdata
Warning messages:
1: no DISPLAY variable so Tk is not available
2: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’
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