| ... | ... |
@@ -1,5 +1,5 @@ |
| 1 | 1 |
% Generated by roxygen2: do not edit by hand |
| 2 |
-% Please edit documentation in R/S3Cover-Param.R |
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| 2 |
+% Please edit documentation in R/S3filter_extract_param.R |
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| 3 | 3 |
\name{filter-extract}
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| 4 | 4 |
\alias{filter-extract}
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| 5 | 5 |
\alias{FULL}
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| ... | ... |
@@ -19,7 +19,7 @@ to be used in filter and extract function. |
| 19 | 19 |
} |
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\details{
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It is used to encompasses all the region parameters already present |
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-into the dataset or GrangesList |
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+into the dataset or GRangesList |
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| 23 | 23 |
|
| 24 | 24 |
\itemize{
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| 25 | 25 |
\item{FULL: It consider all the region paramter}
|
| ... | ... |
@@ -71,8 +71,28 @@ filter_and_extract(test_path, region_attributes = c("pvalue", "peak"))
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| 71 | 71 |
## function makes sure that the region coordinates (chr, ranges, strand) |
| 72 | 72 |
## of all samples are ordered correctly |
| 73 | 73 |
|
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- |
|
| 75 | 74 |
grl <- import_gmql(test_path, TRUE) |
| 76 | 75 |
sorted_grl <- sort(grl) |
| 77 | 76 |
filter_and_extract(sorted_grl, region_attributes = c("pvalue", "peak"))
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+ |
|
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+## It is also possible to define the region attributes, using the FULL() |
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+## function parameter, in order to includes every region |
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+## attributes present into the schema file |
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+ |
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+sorted_grl_full <- sort(grl) |
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+filter_and_extract(sorted_grl, region_attributes = FULL()) |
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+ |
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+grl <- import_gmql(test_path, TRUE) |
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+sorted_grl <- sort(grl) |
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+filter_and_extract(sorted_grl, region_attributes = FULL()) |
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+ |
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+## Also, we can inlcude a list of region attribute inside the FULL() |
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+## function to exlucde that regions |
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+ |
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+sorted_grl_full_except <- sort(grl) |
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+filter_and_extract( |
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+ sorted_grl_full_except, |
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+ region_attributes = FULL("jaccard", "score")
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+) |
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+ |
|
| 78 | 98 |
} |
| ... | ... |
@@ -49,6 +49,21 @@ generated: |
| 49 | 49 |
\item{"provider" = "PoliMi"}
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| 50 | 50 |
\item{"application" = "RGMQL"}
|
| 51 | 51 |
} |
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+ |
|
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+NOTE: |
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+The folder layout must obey the following rules and adopt |
|
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+the following layout: |
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+The dataset folder can have any name, but must contains the |
|
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+sub-folders named: "files". |
|
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+The sub-folder "files" contains the dataset files and |
|
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+the schema xml file. |
|
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+The schema files adopt the following the naming conventions: |
|
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+ |
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+- "schema.xml" |
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+- "test.schema" |
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+ |
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+The names must be in LOWERCASE. Any other schema file |
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+will not be conisdered, if both are present, "test.schema" will be used. |
|
| 52 | 67 |
} |
| 53 | 68 |
\examples{
|
| 54 | 69 |
|
| ... | ... |
@@ -74,4 +89,5 @@ remote_url = "http://www.gmql.eu/gmql-rest/" |
| 74 | 89 |
login_gmql(remote_url) |
| 75 | 90 |
data1 = read_gmql("public.Example_Dataset_1", is_local = FALSE)
|
| 76 | 91 |
|
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+ |
|
| 77 | 93 |
} |
| ... | ... |
@@ -41,6 +41,21 @@ a new dataset is created on remote repository |
| 41 | 41 |
\details{
|
| 42 | 42 |
If no error occurs, it prints "Upload Complete", otherwise a specific error |
| 43 | 43 |
is printed |
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+ |
|
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+NOTE: |
|
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+The folder layout must obey the following rules and adopt |
|
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+the following layout: |
|
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+The dataset folder can have any name, but must contains the |
|
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+sub-folders named: "files". |
|
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+The sub-folder "files" contains the dataset files and |
|
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+the schema xml file. |
|
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+The schema files adopt the following the naming conventions: |
|
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+ |
|
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+- "schema.xml" |
|
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+- "test.schema" |
|
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+ |
|
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+The names must be in LOWERCASE. Any other schema file |
|
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+will not be conisdered, if both are present, "test.schema" will be used. |
|
| 44 | 59 |
} |
| 45 | 60 |
\examples{
|
| 46 | 61 |
|
