segmentstotemplate: Create a template data frame from input that only provides...

In tgac-vumc/ACE: Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

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

tgac-vumc/ACE documentation built on Nov. 29, 2022, 12:15 a.m.