gsa.reshape.concordance.table: Reshape a Concordance Table

Description

Given a GATKReport generated by GenotypeConcordance (as output by gsa.read.gatkreport), this function reshapes the concordance for a specified sample into a matrix with the EvalGenotypes in rows and the CompGenotypes in columns (see the documentation for GenotypeConcordance for the definition of Eval and Comp)

Usage

gsa.reshape.concordance.table(
  report, 
  table.name="GenotypeConcordance_Counts", 
  sample.name="ALL")

Value

Returns a two-dimensional matrix with Eval genotypes in the rows and Comp genotypes in the columns. The genotypes themselves (HOM_REF, NO_CALL, etc) are specified in the row/col names of the matrix.

Arguments

report: A GATKReport as output by gsa.read.gatkreport. If table.name is NULL, report is assumed to be the vector of concordance values to reshape.
table.name: The table name in the GATKReport to reshape. Defaults to "GenotypeConcordance_Counts", but could also be one of the proportion tables ("GenotypeConcordance_EvalProportions", "GenotypeConcordance_CompProportions"). This value can also be NULL, in which case report is reshaped directly.
sample.name: The sample name within table.name to use.

Author

Phillip Dexheimer

Examples

Run this code

test_file = system.file("extdata", "test_genconcord.table", package = "gsalib")
report = gsa.read.gatkreport(test_file)
gsa.reshape.concordance.table(report)

## Output looks like:
##              CompGenotypes
##EvalGenotypes NO_CALL HOM_REF HET HOM_VAR UNAVAILABLE MIXED
##  NO_CALL     0       0       0       0       0           0    
##  HOM_REF     0       0       0       0       0           0    
##  HET         0       0       13463   90      3901        0    
##  HOM_VAR     0       0       2935    18144   4448        0    
##  UNAVAILABLE 0       0       2053693 1326112 11290       0    
##  MIXED       0       0       0       0       0           0