top_integrations: Sorts and keeps the top n integration sites based on the...

In ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Description

\lifecycle

experimental The input data frame will be sorted by the highest values in the columns specified and the top n rows will be returned as output. The user can choose to keep additional columns in the output by passing a vector of column names or passing 2 "shortcuts":

• keep = "everything" keeps all columns in the original data frame

• keep = "nothing" only keeps the mandatory columns (mandatory_IS_vars()) plus the columns in the columns parameter.

Usage

top_integrations(
  x,
  n = 50,
  columns = "fragmentEstimate_sum_RelAbundance",
  keep = "everything",
  key = NULL
)

Arguments

x	An integration matrix (data frame containing mandatory_IS_vars())
n	How many integrations should be sliced (in total or for each group)? Must be numeric or integer and greater than 0
columns	Columns to use for the sorting. If more than a column is supplied primary ordering is done on the first column, secondary ordering on all other columns
keep	Names of the columns to keep besides mandatory_IS_vars() and columns
key	Either NULL or a character vector of column names to group by. If not NULL the input will be grouped and the top fraction will be extracted from each group.

Value

Either a data frame with at most n rows or a data frames with at most n*(number of groups) rows.

See Also

Other Analysis functions: CIS_grubbs(), comparison_matrix(), compute_abundance(), cumulative_count_union(), sample_statistics(), separate_quant_matrices(), threshold_filter()

Examples

smpl <- tibble::tibble(
    chr = c("1", "2", "3", "4", "5", "6"),
    integration_locus = c(14536, 14544, 14512, 14236, 14522, 14566),
    strand = c("+", "+", "-", "+", "-", "+"),
    CompleteAmplificationID = c("ID1", "ID2", "ID1", "ID1", "ID3", "ID2"),
    Value = c(3, 10, 40, 2, 15, 150),
    Value2 = c(456, 87, 87, 9, 64, 96),
    Value3 = c("a", "b", "c", "d", "e", "f")
)
top <- top_integrations(smpl,
    n = 3,
    columns = c("Value", "Value2"),
    keep = "nothing"
)
top_key <- top_integrations(smpl,
    n = 3,
    columns = "Value",
    keep = "Value2",
    key = "CompleteAmplificationID"
)

ISAnalytics documentation built on April 9, 2021, 6:01 p.m.