makeVRangesFromDataFrame: Construct a VRanges Object from a data frame

In YAPSA: Yet Another Package for Signature Analysis

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)

YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.