segmentstotemplate {ACE} | R Documentation

## Create a template data frame from input that only provides segment information

### Description

`segmentstotemplate` "explodes" segment data and creates a data frame with information for all bins. This enables the use of data limited to segments in ACE-related functions.

### Usage

    segmentstotemplate(segmentdf, chrci = 1, startci = 2, endci = 3,
      binsci = 4, meanci = 5, seci, sdci, log = FALSE)

### Arguments

`segmentdf` | Data frame or file path. Data frame or file path to tab-delimited file with segment data
`chrci` | Integer. Specifies the index of the column containing chromosome information. Default = 1
`startci` | Integer. Specifies the index of the column containing start positions. Default = 2
`endci` | Integer. Specifies the index of the column containing end positions. Default = 3
`binsci` | Integer. Specifies the index of the column containing number of bins or number of probes. Default = 4
`meanci` | Integer. Specifies the index of the column containing the segment value. Default = 5
`seci` | Integer. Optional. Specifies the index of the column containing standard errors of the segment mean. See details below
`sdci` | Integer. Optional. Specifies the index of the column containing standard deviations of the segment mean. See details below
`log` | Logical or integer. If the data is given in log-values, the data is converted to linear scale using the given log base, or inverting the natural logarithm when set to TRUE. Default = FALSE

### Details

Even though there is no copy number information for each bin, this needs to be provided for several ACE-related functions. By default, `segmentstotemplate` will just "copy" the segment data. If the segment data comes with either standard deviations or standard errors, it is possible to "simulate" copy number data. To do so, `segmentstotemplate` will use the R stats `rnorm` function.

### Value

Returns a template data frame.

### Note

- Keep in mind that copy number data is used in some functions, notably `ACEcall`. If information on the variance of copy number values within segments is missing, calls are only based on adjusted segment values, because the p-values are all 0.

- Also note that resulting templates should not be used for any of the functions that perform resegmentation (e.g. `twosamplecompare`), or the results should be interpreted with due caution.

- The functions `singlemodel` and `squaremodel` only use segment values and can be used to analyze the resulting template data frames. `singleplot` can also be used without problem.

- This function works fine with high resolution data, but the resulting template can be a bit much for other functions. For instance, the segmented data files provided by TCGA are the result of SNP arrays that have a resolution of roughly 1.5 kbp. The function `compresstemplate` can help out to make input more manageable.

### Author(s)

Jos B. Poell

### See Also

`compresstemplate`

[Package ACE version 1.12.0 Index]