makeVRangesFromDataFrame {YAPSA} | R Documentation |
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
|
in_seqinfo |
A seqInfo object, referring to the reference genome used.
Argument passed on to |
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
data(lymphoma_test) temp_vr <- makeVRangesFromDataFrame(lymphoma_test_df, in_seqnames.field="CHROM", in_subgroup.field="SUBGROUP", verbose_flag=1)