xiaowen chen authored on 20/10/2020 23:52:58
• GitHub committed on 20/10/2020 23:52:58
| ... | ... |
@@ -5,8 +5,8 @@ |
| 5 | 5 |
\title{Calculate Differential Heterogeneity}
|
| 6 | 6 |
\usage{
|
| 7 | 7 |
diffHet(compare.matrix, value, group1, group2, subtype, |
| 8 |
- het.dif.cutoff = 0.2, permutations = 1000, p.adjust.method = "fdr", |
|
| 9 |
- cores = 5) |
|
| 8 |
+ het.dif.cutoff = 0.2, permutations = 1000, permutationtest = FALSE, |
|
| 9 |
+ p.adjust.method = "fdr", cores = 5) |
|
| 10 | 10 |
} |
| 11 | 11 |
\arguments{
|
| 12 | 12 |
\item{compare.matrix}{The comparison matrix generated from
|
| ... | ... |
@@ -35,6 +35,10 @@ to NA. (default: 0.20)} |
| 35 | 35 |
EntropyExplorer function. Value must be set to 'shannon'. |
| 36 | 36 |
(default: 1000)} |
| 37 | 37 |
|
| 38 |
+\item{permutationtest}{boolean values determining if the permutation test is
|
|
| 39 |
+applied for DEH loci identification based on customized heterogeneity metrics |
|
| 40 |
+(default: FALSE)} |
|
| 41 |
+ |
|
| 38 | 42 |
\item{p.adjust.method}{The method to be used as a parameter in
|
| 39 | 43 |
p.adjust() function. Possible methods are 'holm', 'hochberg', |
| 40 | 44 |
'hommel', 'bonferroni', 'BH', 'BY', 'fdr', and 'none'.(default: 'fdr')} |
Mingsheng Zhang authored on 20/11/2018 01:59:38
| ... | ... |
@@ -4,8 +4,9 @@ |
| 4 | 4 |
\alias{diffHet}
|
| 5 | 5 |
\title{Calculate Differential Heterogeneity}
|
| 6 | 6 |
\usage{
|
| 7 |
-diffHet(compare.matrix, value, group1, group2, subtype, het.dif.cutoff = 0.2, |
|
| 8 |
- permutations = 1000, p.adjust.method = "fdr", cores = 5) |
|
| 7 |
+diffHet(compare.matrix, value, group1, group2, subtype, |
|
| 8 |
+ het.dif.cutoff = 0.2, permutations = 1000, p.adjust.method = "fdr", |
|
| 9 |
+ cores = 5) |
|
| 9 | 10 |
} |
| 10 | 11 |
\arguments{
|
| 11 | 12 |
\item{compare.matrix}{The comparison matrix generated from
|
Haitham Ashoor authored on 23/04/2018 17:08:09
| 1 | 1 |
new file mode 100755 |
| ... | ... |
@@ -0,0 +1,56 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/diffHet.R |
|
| 3 |
+\name{diffHet}
|
|
| 4 |
+\alias{diffHet}
|
|
| 5 |
+\title{Calculate Differential Heterogeneity}
|
|
| 6 |
+\usage{
|
|
| 7 |
+diffHet(compare.matrix, value, group1, group2, subtype, het.dif.cutoff = 0.2, |
|
| 8 |
+ permutations = 1000, p.adjust.method = "fdr", cores = 5) |
|
| 9 |
+} |
|
| 10 |
+\arguments{
|
|
| 11 |
+\item{compare.matrix}{The comparison matrix generated from
|
|
| 12 |
+the compMatrix() function} |
|
| 13 |
+ |
|
| 14 |
+\item{value}{The value to be used in calculations. Possible
|
|
| 15 |
+values are 'read', 'pdr', 'meth', 'epipoly', and 'shannon'} |
|
| 16 |
+ |
|
| 17 |
+\item{group1}{The first subtype group to be compared}
|
|
| 18 |
+ |
|
| 19 |
+\item{group2}{The second subtype group to be compared}
|
|
| 20 |
+ |
|
| 21 |
+\item{subtype}{A dataframe containing the subtype information
|
|
| 22 |
+for the samples in the comparison matrix. The row names should |
|
| 23 |
+be the names of the samples and there should be one column |
|
| 24 |
+containing the subtype information for each sample.} |
|
| 25 |
+ |
|
| 26 |
+\item{het.dif.cutoff}{A number representing the cutoff
|
|
| 27 |
+for the heterogeneity difference. If the heterogeneity difference is greater |
|
| 28 |
+than the cutoff value, than the p-value and adjusted p-value are |
|
| 29 |
+calculated for the loci. If the heterogeneity difference is less than |
|
| 30 |
+the cutoff value, than the p-value and adjusted p-value are set |
|
| 31 |
+to NA. (default: 0.20)} |
|
| 32 |
+ |
|
| 33 |
+\item{permutations}{The number of permutations for the
|
|
| 34 |
+EntropyExplorer function. Value must be set to 'shannon'. |
|
| 35 |
+(default: 1000)} |
|
| 36 |
+ |
|
| 37 |
+\item{p.adjust.method}{The method to be used as a parameter in
|
|
| 38 |
+p.adjust() function. Possible methods are 'holm', 'hochberg', |
|
| 39 |
+'hommel', 'bonferroni', 'BH', 'BY', 'fdr', and 'none'.(default: 'fdr')} |
|
| 40 |
+ |
|
| 41 |
+\item{cores}{The number of cores to be used for parallel execution.
|
|
| 42 |
+Not available for 'shannon' values. (default: 5)} |
|
| 43 |
+} |
|
| 44 |
+\value{
|
|
| 45 |
+A dataframe containing chromosome number, loci, mean of |
|
| 46 |
+group1, mean of group2, heterogeneity difference, and the p-value and |
|
| 47 |
+adjusted p-value for the loci with a heterogeneity difference greater |
|
| 48 |
+than the cutoff |
|
| 49 |
+} |
|
| 50 |
+\description{
|
|
| 51 |
+From a user-inputted value and two subtype groups, |
|
| 52 |
+calculates the mean values for both subtypes at each |
|
| 53 |
+loci. The heterogeneity difference is calculated and the p-values |
|
| 54 |
+and adjusted p-values are calculated if the heterogeneity |
|
| 55 |
+difference is greater than a given cutoff |
|
| 56 |
+} |