Biomedical Engineering Reference
In-Depth Information
Summary of usage and operations of the
genomic_scans tool
Table 8.3
Operation
Description
counts
Determines input read counts in sliding windows of
reference regions
peaks
Scans input reads to identify peaks
8.3.4 The permutation_test tool
This tool executes row permutations to determine p-values and q-values
for all the categories contained in the input fi le given the statistic chosen
by the user (see Table 8.4 for available statistical tests). More specifi cally,
the statistic on the set of rows annotated by a given category is compared
against the same statistic on permuted versions of the input on the value
column. For an example, see
Identifying enriched Gene Ontology terms
.
8.3.5 Vector and matrix operations
The GenomicTools distribution includes two command-line tools for
manipulating labeled vectors and matrices. The input format for the
vectors command-line tool is a series of lines, each of which has two
TAB-separated fi elds (label and SPACE-separated vector elements).
The label fi eld is optional. Similarly, the input format of the matrix
Table 8.4
Supported statistics for the permutation tests
Statistic
Description
sum
The sum of values in a given category
n
Number of values > 0
sens
Sensitivity
spec
Specifi city
ratio
Mean of values divided by mean of values in the background
t
t-test between mean of values against mean of values in the
background
Search WWH ::
Custom Search