| ... | ... |
@@ -52,7 +52,7 @@ CNE(assembly1Fn=character(1), assembly2Fn=character(1), |
| 52 | 52 |
\item{CNE12}{Object of class \code{"GRangePairs"}:
|
| 53 | 53 |
The preliminary CNEs from axt file with assembly1 as reference.} |
| 54 | 54 |
\item{CNE21}{Object of class \code{"GRangePairs"}:
|
| 55 |
- The preliminart CNEs from axt file with assembly2 as reference.} |
|
| 55 |
+ The preliminary CNEs from axt file with assembly2 as reference.} |
|
| 56 | 56 |
\item{CNEMerged}{Object of class \code{"GRangePairs"}:
|
| 57 | 57 |
The CNEs after merging CNE1 and CNE2.} |
| 58 | 58 |
\item{CNEFinal}{Object of class \code{"GRangePairs"}:
|
| ... | ... |
@@ -33,20 +33,20 @@ |
| 33 | 33 |
} |
| 34 | 34 |
\item{background}{
|
| 35 | 35 |
\code{character}(1):
|
| 36 |
- can be "chromosome" or "genome". When slice the CNE density, |
|
| 36 |
+ can be "chromosome" or "genome". When using \code{slice} for the CNE density,
|
|
| 37 | 37 |
the background is calculated on a per-chromosome or whole-genome basis. |
| 38 | 38 |
} |
| 39 | 39 |
\item{minCNEs}{
|
| 40 |
- \code{integer}(1): the minimal number of CNEs that a GRB need to have.
|
|
| 40 |
+ \code{integer}(1): the minimal number of CNEs that a GRB needs to have.
|
|
| 41 | 41 |
} |
| 42 | 42 |
} |
| 43 | 43 |
\details{
|
| 44 |
- First we calculated the CNE densities from the CNEs. |
|
| 44 |
+ First we calculate the CNE densities from the CNEs. |
|
| 45 | 45 |
Then we segment the regions according to the values of CNE densities. |
| 46 | 46 |
The regions with CNE densities above the expected CNE densities * ratio are |
| 47 | 47 |
considered as putative GRBs. |
| 48 |
- Of course, the putative GRBs that do not encompass any gene are filtered out. |
|
| 49 |
- Finanlly, the GRBs that have fewered than \code{minCNEs} number of CNEs will
|
|
| 48 |
+ Putative GRBs that do not encompass any gene are filtered out. |
|
| 49 |
+ Finally, the GRBs that have fewer than \code{minCNEs} number of CNEs will
|
|
| 50 | 50 |
be filtered out. |
| 51 | 51 |
} |
| 52 | 52 |
\value{
|
| ... | ... |
@@ -6,8 +6,8 @@ |
| 6 | 6 |
} |
| 7 | 7 |
\description{
|
| 8 | 8 |
CNE widths can follow heavy tailed distribution that are associated with power-laws. |
| 9 |
- This function plot the reverse cumulative density distribution of CNE widths, |
|
| 10 |
- and fit a discrete power-law distribution. |
|
| 9 |
+ This function plots the reverse cumulative density distribution of CNE widths, |
|
| 10 |
+ and fits a discrete power-law distribution. |
|
| 11 | 11 |
Goodness of fit can also be evaluated. |
| 12 | 12 |
} |
| 13 | 13 |
\usage{
|
| ... | ... |
@@ -1,10 +1,10 @@ |
| 1 | 1 |
\name{read.rmskFasta}
|
| 2 | 2 |
\alias{read.rmskFasta}
|
| 3 | 3 |
\title{
|
| 4 |
- Read a soft reoeat masked fasta |
|
| 4 |
+ Read a soft repeat masked fasta |
|
| 5 | 5 |
} |
| 6 | 6 |
\description{
|
| 7 |
- Read a soft repeat masked fasta file into a \code{GRanges}.
|
|
| 7 |
+ Read a soft repeat masked fasta file into a \code{GRanges} object.
|
|
| 8 | 8 |
} |
| 9 | 9 |
\usage{
|
| 10 | 10 |
read.rmskFasta(fn) |
| ... | ... |
@@ -5,7 +5,7 @@ |
| 5 | 5 |
Read the cne file from Ancora format. |
| 6 | 6 |
} |
| 7 | 7 |
\description{
|
| 8 |
- Read the Ancora CNE file into a \code{GRanges} or \code{GRangePairs}.
|
|
| 8 |
+ Read the Ancora CNE file into a \code{GRanges} or \code{GRangePairs} object.
|
|
| 9 | 9 |
} |
| 10 | 10 |
\usage{
|
| 11 | 11 |
readAncora(fn, assembly=NULL, tAssemblyFn=NULL, qAssemblyFn=NULL) |
| ... | ... |
@@ -6,7 +6,7 @@ |
| 6 | 6 |
} |
| 7 | 7 |
\description{
|
| 8 | 8 |
Query the SQLite database based on chromosome, |
| 9 |
-coordinates and some other criterias. |
|
| 9 |
+coordinates and some other criteria. |
|
| 10 | 10 |
Primarily not intended to be used directly. |
| 11 | 11 |
For the CNE density plot, \code{fetchCNEDensity} function should be used.
|
| 12 | 12 |
} |
| ... | ... |
@@ -15,7 +15,7 @@ |
| 15 | 15 |
\item{distance}{
|
| 16 | 16 |
It can be "far", "medium" or "close". It defines the scoring matrix used in |
| 17 | 17 |
\emph{lastz} aligner.
|
| 18 |
- Generally, if two species are close to each other at human and chimp level, |
|
| 18 |
+ Generally, if two species are close to each other, for example human and chimp, |
|
| 19 | 19 |
"close" should be used. |
| 20 | 20 |
If two species have a divergence time of 100 MYA, "far" should be used. |
| 21 | 21 |
In other cases, "medium" should be used. |
