View source: R/internal_read_maf.R
read_in_maf | R Documentation |
Load MAF data from a text file or data table into your CESAnalysis. If column names
don't match MAF format specifications (Chromosome, Start_Position, etc., with
Tumor_Sample_Barcode used as the sample ID column), you can supply your own column
names. When your CESAnalysis has defined sample groups (see ?CESAnalysis
),
specify "group_col". By default, data is assumed to be derived from whole-exome
sequencing. Whole-genome data and targeted sequencing data are also supported when the
"coverage" option is specified. If the data you are loading is from a different genome
build than your CESAnalysis, you can use the "chain_file" option to supply a UCSC-style
chain file, and your MAF coordinates will be automatically converted with
rtracklayer's version of liftOver.
read_in_maf(
maf,
refset_env,
chr_col = "Chromosome",
start_col = "Start_Position",
ref_col = "Reference_Allele",
tumor_allele_col = "guess",
sample_col = "Unique_Patient_Identifier",
more_cols = NULL,
chain_file = NULL,
separate_old_problems = FALSE
)
maf |
Path of tab-delimited text file in MAF format, or an MAF in data.table or data.frame format |
refset_env |
a refset data environment |
chr_col |
column name with chromosome data (Chromosome) |
start_col |
column name with start position (Start_Position) |
ref_col |
column name with reference allele data (Reference_Allele) |
tumor_allele_col |
column name with alternate allele data; by default, values from Tumor_Seq_Allele2 and Tumor_Seq_Allele1 columns are used. |
sample_col |
column name with sample ID data (Tumor_Sample_Barcode or Unique_Patient_Identifier) |
chain_file |
a LiftOver chain file (text format, name ends in .chain) to convert MAF records to the genome build used in the CESAnalysis. |
separate_old_problems |
When TRUE (as used by load_maf), respect old problems that look like they came from cancereffectsizeR (typically from preload_maf). These get separated as "old_problem", and the records won't be checked. chain_file must be NULL. |
data.table with core MAF columns, any other requested columns, and a "problem" column
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