makeVRangesFromDataFrame: Construct a VRanges Object from a data frame
In eilslabs/YAPSA: Yet Another Package for Signature Analysis

Description Usage Arguments Value See Also Examples

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

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)

`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

The constructed VRanges object

makeGRangesFromDataFrame

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