diff --git a/index.html b/index.html index cae5e89..fe51b90 100644 --- a/index.html +++ b/index.html @@ -77,8 +77,8 @@

InstallationSystem dependencies

-

-htslib +

+htslib >= 1.19

iscream depends on the htslib header files. These may be installed with your package manager:

-

They may also be found among your HPC modules - make sure the PKG_CONFIG_PATH environment variable includes the pkgconfig location for your installation of htslib. You can verify that the htslib development libraries are installed with pkg-config:

+

or built manually: https://www.htslib.org/download/.

+

The header files may also be found among your HPC modules - make sure the PKG_CONFIG_PATH environment variable includes the pkgconfig location for your installation of htslib. You can verify that the htslib development libraries are installed with pkg-config:

pkg-config --cflags --libs htslib
diff --git a/pkgdown.yml b/pkgdown.yml index 5af5840..6b1609a 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.11 pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2024-12-04T20:03Z +last_built: 2024-12-04T20:15Z urls: reference: https://huishenlab.github.io/iscream/reference article: https://huishenlab.github.io/iscream/articles diff --git a/reference/get_df_string.html b/reference/get_df_string.html new file mode 100644 index 0000000..d00a7dd --- /dev/null +++ b/reference/get_df_string.html @@ -0,0 +1,81 @@ + +DataFrame to region strings — get_df_string • iscream + Skip to contents + + +
+
+
+

DataFrame to region strings

+ Source: R/utils.R +
get_df_string.Rd
+
+ +
+

Convert DataFrame to a vector of strings. Set feature names in a "name" column

+
+ +
+

Usage

+ 
get_df_string(regions_df)
+
+ +
+

Arguments

+ + +
regions_df
+

A data frame with "chr", "start" and "end" columns

+ +
+
+

Value

+

A character vector

+
+ +
+ + +
+

Developed by James Eapen.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + diff --git a/reference/index.html b/reference/index.html index b293fe1..d7ba903 100644 --- a/reference/index.html +++ b/reference/index.html @@ -93,6 +93,12 @@

Utilitiesget_df_string() + + +
DataFrame to region strings

Settings

diff --git a/reference/query_all.html b/reference/query_all.html index a37f7b7..671362b 100644 --- a/reference/query_all.html +++ b/reference/query_all.html @@ -72,7 +72,8 @@

Argumentsregions -

A vector of genomic regions strings

+

A vector, data frame or GenomicRanges of genomic regions. See +details.

aligner
@@ -107,6 +108,12 @@

Value

  • a character vector of the input sample names

    • +
    +

    Details

    +

    The input regions may be string vector in the form "chr:start-end" +or a GRanges object. If a data frame is provided, they must have "chr", +"start", and "end" columns.

    +

    Examples

    @@ -163,11 +170,11 @@

    Examples# make a vector of regions regions <- c("chr1:1-6", "chr1:7-10", "chr1:11-14") query_all(bedfiles, regions) -#> [20:03:24.709549] [iscream::query_all] [info] Querying 3 regions from 4 bedfiles +#> [20:16:03.406446] [iscream::query_all] [info] Querying 3 regions from 4 bedfiles #> -#> [20:03:24.709977] [iscream::query_all] [info] Creating metadata vectors -#> [20:03:24.710029] [iscream::query_all] [info] nrows 10000 - 9993 extra rows allocated with 0 resizes -#> [20:03:24.710035] [iscream::query_all] [info] Creating dense matrix +#> [20:16:03.406856] [iscream::query_all] [info] Creating metadata vectors +#> [20:16:03.406906] [iscream::query_all] [info] nrows 10000 - 9993 extra rows allocated with 0 resizes +#> [20:16:03.406911] [iscream::query_all] [info] Creating dense matrix #> $M #> a b c d #> chr1:2 1 0 0 1 diff --git a/reference/summarize_regions.html b/reference/summarize_regions.html index 521e6c8..40f7326 100644 --- a/reference/summarize_regions.html +++ b/reference/summarize_regions.html @@ -66,9 +66,8 @@

    Argumentsregions -

    A vector of genomic regions strings. If a named vector is -provided, the names will be used in the feature column instead of the -genomic regions string

    +

    A vector, data frame or GenomicRanges of genomic regions. See +details.

    fun
    @@ -87,8 +86,8 @@

    Argumentsset_region_rownames

    Use the region strings as the returned data -frame's rownames. Can be useful if you have a named vector of regions and -want both the rownames and the feature names.

    +frame's rownames. Can be useful if you have a named regions and want both +the regions strings rownames and the feature names.

    nthreads
    @@ -102,7 +101,13 @@

    Value

    Details

    -

    Supported fun arguments are given below. For each of these functions, +

    The input regions may be string vector in the form "chr:start-end" +or a GRanges object. If a data frame is provided, they must have "chr", +"start", and "end" columns. If the string vector and GenomicRanges inputs +are named, the names will be used to describe each feature in the output +dataframe. If input dataframes have a 'name' column, it will be used to +populate the output's feature column.

    +

    Supported fun arguments are given below. For each of these functions, setting mval = FALSE will use the beta values instead of the M value: