Description Usage Arguments Value Author(s)
Creates the hard filtered final dataframe by removing PON, cFilter, soft clipped and hard clipped filtered data from the input dataframe.
1 | create_final_filtered_dataframe(data = NULL, pon_threshold = 1, flagged_threshold = 1, soft_threshold = 0, hard_threshold = 0)
|
data |
dataframe containing the annotated SNV data (required) |
pon_threshold |
the number of recurrent normal samples a mutation is found in (default: 1) |
flagged_threshold |
the number of flagged filters a mutation is found in (default: 1) |
soft_threshold |
the maximum number of reads a mutation can be found in a soft clipped region (default: 0) |
hard_threshold |
the maximum number of reads a mutation can be found in a hard clipped region (default: 0) |
Returns a dataframe containing hard filtered SNVs.
Richard J. de Borja <richard.deborja@sickkids.ca>
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