fg_add_summary {flowGraph} | R Documentation

## Adds a feature summary.

### Description

Adds a feature summary into a given flowGraph object. Only use this function if your summary statistic cannot be calcuated using the `fg_summary` function.

### Usage

    fg_add_summary(
      fg,
      type = "node",
      summary_meta = NULL,
      p = NULL,
      summ_fun = NULL,
      overwrite = FALSE,
      ...
    )

### Arguments

`fg` | flowGraph object.
`type` | A string indicating feature type the summary was created for; 'node' or 'edge'.
`summary_meta` | The user must provide `type` and `summary_meta`. `summary_meta` is a list containing `feature` (feature name), `test_name` (summary statistic name), `class` (class), `label1`, and `label2` (class labels compared). See `fg_get_summary_desc` for details.
`p` | A list containing summary values; this list contains elements: `values` (a vector containing summary statistics e.g. p-values; this vector should be named by their associated phenotype or edge name), `test_custom` (a function of the statistical test used), and `adjust_custom` (a function of the p-value correction method used). This list must contain the `values` element.
`summ_fun` | A function that ouputs a feature summary matrix as in `p` given `fg` and other optional parameters.
`overwrite` | A logical variable indicating whether or not the function should replace the existing feature summary with the same name if one is already in `fg`.
`...` | Other parameters that would be used as input into `summ_fun`.

### Details

`fg_add_summary` adds the given feature summary list `p` or the output of the given function `summ_fun` to the given flowGraph object `fg` updating slots `summary` and `summary_desc`. See `flowGraph-class` slot `summary` and `summary_desc` for what should be in these slots. We do not recommend users directly use this function unless what is required is duly in the above slots is well understood — note these slots are used in plotting functions e.g. `fg_plot`. We instead recommend users to use the `fg_summary` function.

### Value

flowGraph object.

### See Also

`flowGraph-class` `fg_summary` `fg_get_summary` `fg_rm_summary` `fg_get_summary_desc` `fg_add_feature`

### Examples

     no_cores <- 1
     data(fg_data_pos30)
     fg <- flowGraph(fg_data_pos30$count, class=fg_data_pos30$meta$class,
                     no_cores=no_cores)

     # get samples that we are going to compare
     m <- fg_get_feature(fg, type="node", feature="prop")
     m1_ <- m[fg_data_pos30$meta$class=="control",,drop=FALSE]
     m2_ <- m[fg_data_pos30$meta$class=="exp",,drop=FALSE]

     # define test or summary function to conduct comparison
     test_custom <- function(x,y)
         tryCatch(stats::t.test(x,y)$p.value, error=function(e) 1)
     values_p <- sapply(seq_len(ncol(m)), function(j)
         test_custom(m1_[,j], m2_[,j]) )
     values_p <- p.adjust(values_p , method="BY")

     # the user can choose to fill either parameter "p" or "summ_fun",
     # the latter of which must output a list with the same elements as "p".
     # see documentation for ?flowGraph-class, slot "summary" for
     # details on what should be in "p".
     p <- list(values=values_p, test_fun=test_custom, adjust_fun="BY")
     fg <- fg_add_summary(fg, type="node", summary_meta=list(
          feature="prop", test_name="wilcox_BY",
          class="class", label1="control", label2="exp"), p=p)

     fg_get_summary_desc(fg)

[Package flowGraph version 1.2.0 Index]