compute_abundance {ISAnalytics} | R Documentation |
Abundance is obtained for every integration event by calculating the ratio
between the single value and the total value for the given group.
compute_abundance( x, columns = c("fragmentEstimate_sum"), percentage = TRUE, key = c("SubjectID", "CellMarker", "Tissue", "TimePoint"), keep_totals = FALSE )
x |
An integration matrix - aka a data frame that includes
the |
columns |
A character vector of column names to process, must be numeric or integer columns |
percentage |
Add abundance as percentage? |
key |
The key to group by when calculating totals |
keep_totals |
A value between |
Abundance will be computed upon the user selected columns
in the columns
parameter. For each column a corresponding
relative abundance column (and optionally a percentage abundance
column) will be produced.
Either a single data frame with computed abundance values or a list of 2 data frames (abundance_df, quant_totals)
Other Analysis functions:
CIS_grubbs()
,
comparison_matrix()
,
cumulative_count_union()
,
cumulative_is()
,
is_sharing()
,
purity_filter()
,
sample_statistics()
,
separate_quant_matrices()
,
threshold_filter()
,
top_integrations()
data("integration_matrices", package = "ISAnalytics") abund <- compute_abundance( x = integration_matrices, columns = "fragmentEstimate", key = "CompleteAmplificationID" ) head(abund)