Simone authored on 09/06/2019 11:05:22
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@@ -3,29 +3,17 @@ |
| 3 | 3 |
\name{AGGREGATES-Object}
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| 4 | 4 |
\alias{AGGREGATES-Object}
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| 5 | 5 |
\alias{SUM}
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-\alias{AGGREGATES-Object}
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\alias{COUNT}
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-\alias{AGGREGATES-Object}
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\alias{COUNTSAMP}
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-\alias{AGGREGATES-Object}
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\alias{MIN}
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-\alias{AGGREGATES-Object}
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\alias{MAX}
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-\alias{AGGREGATES-Object}
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\alias{AVG}
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-\alias{AGGREGATES-Object}
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\alias{MEDIAN}
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-\alias{AGGREGATES-Object}
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| 19 | 12 |
\alias{STD}
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-\alias{AGGREGATES-Object}
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| 21 | 13 |
\alias{BAG}
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-\alias{AGGREGATES-Object}
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\alias{BAGD}
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-\alias{AGGREGATES-Object}
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\alias{Q1}
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-\alias{AGGREGATES-Object}
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\alias{Q2}
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-\alias{AGGREGATES-Object}
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\alias{Q3}
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\title{AGGREGATES object class constructor}
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| 31 | 19 |
\usage{
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@@ -4,15 +4,10 @@ |
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\alias{DISTAL-Object}
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| 5 | 5 |
\alias{DL}
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\alias{DG}
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-\alias{DISTAL-Object}
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\alias{DLE}
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-\alias{DISTAL-Object}
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\alias{DGE}
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-\alias{DISTAL-Object}
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\alias{MD}
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-\alias{DISTAL-Object}
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| 14 | 10 |
\alias{UP}
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-\alias{DISTAL-Object}
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\alias{DOWN}
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| 17 | 12 |
\title{DISTAL object class constructor}
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| 18 | 13 |
\usage{
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@@ -46,7 +46,8 @@ from filtering. |
| 46 | 46 |
} |
| 47 | 47 |
\details{
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| 48 | 48 |
This function works only with datatset or GRangesList all whose samples or |
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-Granges have the same region coordinates (chr, ranges, strand) |
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+Granges have the same region coordinates (chr, ranges, strand) ordered in |
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+the same way for each sample |
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| 50 | 51 |
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In case of GRangesList data input, the function searches for metadata |
| 52 | 53 |
into metadata() function associated to GRangesList. |
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@@ -61,10 +62,14 @@ test_path <- system.file("example", "DATASET", package = "RGMQL")
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| 61 | 62 |
filter_and_extract(test_path, region_attributes = c("pvalue", "peak"))
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| 62 | 63 |
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## This statement imports a GMQL dataset as GRangesList and filters it |
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-## including at output only "pvalue" and "peak" region attributes |
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+## including at output only "pvalue" and "peak" region attributes, the sort |
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+## function makes sure that the region coordinates (chr, ranges, strand) |
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+## of all samples are ordered correctly |
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+ |
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| 65 | 69 |
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grl = import_gmql(test_path, TRUE) |
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-filter_and_extract(grl, region_attributes = c("pvalue", "peak"))
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+sorted_grl = sort(grl) |
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+filter_and_extract(sorted_grl, region_attributes = c("pvalue", "peak"))
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| 68 | 73 |
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| 69 | 74 |
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} |
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@@ -4,8 +4,8 @@ |
| 4 | 4 |
\alias{init_gmql}
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\title{Init GMQL server}
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\usage{
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-init_gmql(output_format = "GTF", remote_processing = FALSE, url = NULL, |
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- username = NULL, password = NULL) |
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+init_gmql(output_format = "GTF", remote_processing = FALSE, |
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+ url = NULL, username = NULL, password = NULL) |
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| 9 | 9 |
} |
| 10 | 10 |
\arguments{
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| 11 | 11 |
\item{output_format}{string that identifies the output format of all sample
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@@ -22,3 +22,12 @@ After logout the authentication token will be invalidated. |
| 22 | 22 |
The authentication token is removed from R Global environment. |
| 23 | 23 |
If error occurs, a specific error is printed |
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} |
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+\examples{
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+ |
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+## Login to GMQL REST services suite as guest, then logout |
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+ |
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+remote_url = "http://www.gmql.eu/gmql-rest/" |
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+login_gmql(remote_url) |
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+logout_gmql(remote_url) |
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+ |
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+} |
| ... | ... |
@@ -4,13 +4,13 @@ |
| 4 | 4 |
\name{map}
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\alias{map}
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\alias{map,GMQLDataset-method}
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-\alias{map}
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\alias{map-method}
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\title{Method map}
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\usage{
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| 11 | 10 |
map(x, y, ...) |
| 12 | 11 |
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-\S4method{map}{GMQLDataset}(x, y, ..., joinBy = conds(), count_name = "")
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+\S4method{map}{GMQLDataset}(x, y, ..., joinBy = conds(),
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+ count_name = "") |
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} |
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\arguments{
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\item{x}{GMQLDataset class object}
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| ... | ... |
@@ -6,8 +6,9 @@ |
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\alias{merge,GMQLDataset,GMQLDataset-method}
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\title{Method merge}
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\usage{
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-\S4method{merge}{GMQLDataset,GMQLDataset}(x, y, genometric_predicate = NULL,
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- region_output = "CAT", joinBy = conds(), reg_attr = c(""))
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+\S4method{merge}{GMQLDataset,GMQLDataset}(x, y,
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+ genometric_predicate = NULL, region_output = "CAT", |
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+ joinBy = conds(), reg_attr = c(""))
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} |
| 12 | 13 |
\arguments{
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\item{x}{GMQLDataset class object}
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