top_integrations {ISAnalytics} | R Documentation

## 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 = 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"
    )

[Package ISAnalytics version 1.0.11 Index]