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

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

Sorts and keeps the top n integration sites based on the values in a given column.

Description

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 = 20,
  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.

Required tags

The function will explicitly check for the presence of these tags:

• All columns declared in mandatory_IS_vars()

See Also

Other Analysis functions: CIS_grubbs(), HSC_population_size_estimate(), compute_abundance(), cumulative_is(), gene_frequency_fisher(), is_sharing(), iss_source(), sample_statistics(), top_targeted_genes()

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"
)

calabrialab/ISAnalytics documentation built on Dec. 10, 2024, 10:50 p.m.