create_SCNA_score_df | R Documentation |
Create SCNA Score Data Frame
create_SCNA_score_df(
gene_SCNA_df,
build = "GRCh37",
log2_ratio_threshold = 0.25,
MCR_overlap_threshold = 25
)
gene_SCNA_df |
data frame of gene-level SCNAs (output of |
build |
genome build for the SCNA segments data frame (default = "GRCh37") |
log2_ratio_threshold |
the log2 ratio threshold for keeping high-confidence SCNA events (default = 0.25) |
MCR_overlap_threshold |
the percentage threshold for the overlap between a gene and an MCR region (default = 25). This means that if only a gene overlaps an MCR region more than this threshold, the gene is assigned the SCNA density of the MCR |
The function first aggregates SCNA log2 ratio on gene-level (by keeping the ratio with the maximal |log2| ratio over all the SCNA segments overlapping a gene). Next, it identifies the minimal common regions (MCRs) that the genes overlap and finally assigns the SCNA density (SCNA/Mb) values as proxy SCNA scores.
data frame of SCNA proxy scores containing 2 columns:
HGNC gene symbol
SCNA proxy score. SCNA density (SCNA/Mb) of the minimal common region (MCR) in which the gene is located.
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