Function used to generate a DEprot object starting from counts and metadata.
load.counts2(
counts,
metadata,
data.type,
log.base,
normalization.method = NA,
randomization.method = NA,
imputation.method = NA,
column.id = "column.id",
protein.info = NULL,
protein.info.id.column = NULL
)A data.frame or a matrix in which the rownames are the proteins and the columns the samples.
A data.frame containing at least one column called column.id which corresponds to the colnames of counts. Any other column can be added and will correspond to a "feature"of each sample.
String indicating the type of data that are loaded. One among: 'raw', 'normalized', 'randomized', 'imputed'.
Number indicating the base of the log used to transform the counts. If none transformation is applied, indicate the base 1. By default, the output data are always transformed in log2 base.
String or list indicating the normalization method used. If none, use the default value NA.
String or list indicating the randomization method used. If none, use the default value NA.
A string indicating the imputation method used. If none, use the default value NA.
String indicating the name of the column to use as "column.id" from the metadata data.frame. This column must contain all the colnames of counts.
Optional data.frame (or matrix) with one row per protein and any number of annotation columns (e.g., gene symbol, description, number of peptides). The protein IDs must be provided as row names, in a column called prot.id, or in the column indicated by protein.info.id.column; they must correspond to the row names of counts. The table is re-ordered to match the counts: proteins missing from the annotation are filled with NA, annotations of proteins absent from the counts are discarded. Default: NULL (no annotation).
String indicating the name of the column of protein.info containing the protein IDs. If NULL (default), the row names are used (or a column called prot.id when the table has no explicit row names).
A DEprot object (S4 vector).
dpo <- load.counts2(counts = DEprot::unimputed.counts,
metadata = DEprot::sample.config,
log.base = 2,
data.type = "raw")
#> The counts matrix contained 295 rows with only NA values.
#> The latter have been removed from the matrix.