readSegment {MesKit} | R Documentation

## readSegment

### Description

readSegment

### Usage

    readSegment(
      segFile,
      gisticAmpGenesFile = NULL,
      gisticDelGenesFile = NULL,
      gisticAllLesionsFile = NULL,
      gistic.qval = 0.25,
      min.seg.size = 500,
      txdb = NULL,
      min.overlap.len = 50,
      verbose = TRUE,
      ...
    )

### Arguments

`segFile` | The segment file.
`gisticAmpGenesFile` | Amplification Genes file generated by GISTIC. Default NULL.
`gisticDelGenesFile` | Deletion Genes file generated by GISTIC. Default NULL.
`gisticAllLesionsFile` | Information of all lesions generated by GISTIC. Default NULL.
`gistic.qval` | The threshold of gistic Q value. Default 0.25.
`min.seg.size` | The smallest size of segments. Default 500.
`txdb` | A TxDb object. i.e., TxDb.Hsapiens.UCSC.hg19.knownGene. Default NULL.
`min.overlap.len` | The minimum insertion size of segment and gene. Default 50.
`verbose` | Whether to display details in the console. Default TRUE.
`...` | ... Other options passed to `cna2gene`.

### Value

a list of segmentation data frame

### Examples

    segFile <- system.file("extdata", "CRC_HZ.seg.txt", package = "MesKit")
    gisticAmpGenesFile <- system.file("extdata", "COREAD_amp_genes.conf_99.txt", package = "MesKit")
    gisticDelGenesFile <- system.file("extdata", "COREAD_del_genes.conf_99.txt", package = "MesKit")
    gisticAllLesionsFile <- system.file("extdata", "COREAD_all_lesions.conf_99.txt", package = "MesKit")
    seg <- readSegment(segFile = segFile,
                       gisticAmpGenesFile = gisticAmpGenesFile,
                       gisticDelGenesFile = gisticDelGenesFile,
                       gisticAllLesionsFile = gisticAllLesionsFile)

[Package MesKit version 1.4.0 Index]