makeVRangesFromDataFrame {YAPSA} | R Documentation

## Construct a VRanges Object from a data frame

### Description

In this package, big data frames are generated from cohort wide vcf-like files. This function constructs a VRanges object from such a data frame by using `makeGRangesFromDataFrame` from the package `GenomicRanges`

### Usage

    makeVRangesFromDataFrame(
      in_df,
      in_keep.extra.columns = TRUE,
      in_seqinfo = NULL,
      in_seqnames.field = "X.CHROM",
      in_start.field = "POS",
      in_end.field = "POS",
      in_PID.field = "PID",
      in_subgroup.field = "subgroup",
      in_strand.field = "strand",
      verbose_flag = 1
    )

### Arguments

`in_df` | A big dataframe constructed from a vcf-like file of a whole cohort. The first columns are those of a standard vcf file, followed by an arbitrary number of custom or user defined columns. One of these can carry a PID (patient or sample identifyier) and one can carry subgroup information.
`in_keep.extra.columns` | in_seqinfo Argument passed on to `makeGRangesFromDataFrame`
`in_seqinfo` | A seqInfo object, referring to the reference genome used. Argument passed on to `makeGRangesFromDataFrame`
`in_seqnames.field` | Indicates the name of the column in which the chromosome is encoded
`in_start.field` | Indicates the name of the column in which the start coordinate is encoded
`in_end.field` | Indicates the name of the column in which the end coordinate is encoded
`in_PID.field` | Indicates the name of the column in which the PID (patient or sample identifier) is encoded
`in_subgroup.field` | Indicates the name of the column in which the subgroup information is encoded
`in_strand.field` | Indicates the name of the column in which the strandedness is encoded
`verbose_flag` | Verbose if 1

### Value

The constructed VRanges object

### See Also

`makeGRangesFromDataFrame`

### Examples

     data(lymphoma_test)
     temp_vr <- makeVRangesFromDataFrame(lymphoma_test_df,
                                         in_seqnames.field="CHROM",
                                         in_subgroup.field="SUBGROUP",
                                         verbose_flag=1)

[Package YAPSA version 1.16.0 Index]