exome: Exome annotation for human genome build NCBI 36/hg18

In kdkorthauer/MADGiC: Fits an empirical Bayesian hierarchical model to obtain posterior probabilities that each gene is a driver.

Description

This data set contains a list with an item for each chromosome where each item is a matrix with a row for each position and 15 columns that contain information about how many of each type of mutation are possible, what their FI (functional impact, here we use SIFT scores) are, and whether each type of change is nonsilent. This object is broken down into 3 objects in the function get.post.probs, each containing columns 1, 2, and 7: exome.constants (and columns 3-6), exome.SIFT (and columns 8:11), and exome.nonsil (and columns 12-15).

Format

Each list item (one per chromosome) contains a matrix with one row per position and the following 15 columns: 1 - base pair position, 2 -ame nucleotide (integer representation, see convert.seq.to.num), 3 - number of possible nonsilent transitions, 4 - number of possible nonsilent transversions, 5 - number of possible silent transitions, 6 - number of possible silent transversions, 7 - indicator of whether position is in a CpG dinucleotide, 8 - FI score for mutation to "A", 9 -FI score for mutation to "C", 10 - FI score for mutation to "G", 11 - FI score for mutation to "T", 12 - nonsilent indicator (1=nonsilent, 0=silent) for mutation to "A", 13 - nonsilent indicator for mutation to "C", 14 - nonsilent indicator for mutation to "G", and 15 - nonsilent indicator for mutation to "T".

kdkorthauer/MADGiC documentation built on June 13, 2020, 1:35 p.m.