vignettes/mia.Rmd
+ Source: vignettes/mia.Rmd
mia.RmdBorman T, Ernst F, Shetty S, Lahti L (2024). mia: Microbiome analysis. -R package version 1.15.1, https://github.com/microbiome/mia. +R package version 1.15.0, https://github.com/microbiome/mia.
@Manual{,
title = {mia: Microbiome analysis},
author = {Tuomas Borman and Felix G.M. Ernst and Sudarshan A. Shetty and Leo Lahti},
year = {2024},
- note = {R package version 1.15.1},
+ note = {R package version 1.15.0},
url = {https://github.com/microbiome/mia},
}
diff --git a/index.html b/index.html
index 92d6e8b82..8a9707f99 100644
--- a/index.html
+++ b/index.html
@@ -33,7 +33,7 @@
diff --git a/pkgdown.yml b/pkgdown.yml
index 2ad679e05..710c21aca 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,4 +3,4 @@ pkgdown: 2.1.1
pkgdown_sha: ~
articles:
mia: mia.html
-last_built: 2024-11-01T08:02Z
+last_built: 2024-11-01T08:05Z
diff --git a/reference/GlobalPatterns.html b/reference/GlobalPatterns.html
index 7825f6821..aac230dfb 100644
--- a/reference/GlobalPatterns.html
+++ b/reference/GlobalPatterns.html
@@ -24,7 +24,7 @@
@@ -51,7 +51,7 @@
R/estimateDivergence.R
+ Source: R/estimateDivergence.R
addDivergence.RdR/agglomerate.R, R/splitByRanks.R
+ Source: R/agglomerate.R, R/splitByRanks.R
agglomerate-methods.RdR/getPrevalence.R
+ Source: R/getPrevalence.R
agglomerateByPrevalence.RdR/calculateDMM.R
+ Source: R/calculateDMM.R
calculateDMN.RdTreeSummarizedExperiment object from ‘DADA2’ resultsR/convertFromDADA2.R
+ Source: R/convertFromDADA2.R
convertFromDADA2.RdTreeSummarizedExperiment object from a phyloseq objectR/convertFromPhyloseq.R, R/convertToPhyloseq.R
+ Source: R/convertFromPhyloseq.R, R/convertToPhyloseq.R
convertFromPhyloseq.RdR/deprecate.R
+ Source: R/deprecate.R
deprecate.RdR/getCrossAssociation.R
+ Source: R/getCrossAssociation.R
getCrossAssociation.RdR/addDissimilarity.R
+ Source: R/addDissimilarity.R
getDissimilarity.RdR/getPrevalence.R
+ Source: R/getPrevalence.R
getPrevalence.RdTreeSummarizedExperiment object to/from ‘BIOM’ resultsR/convertFromBIOM.R
+ Source: R/convertFromBIOM.R
importBIOM.RdTreeSummarizedExperimentR/importHumann.R
+ Source: R/importHumann.R
importHUMAnN.RdTreeSummarizedExperimentR/importMetaphlan.R
+ Source: R/importMetaphlan.R
importMetaPhlAn.RdTreeSummarizedExperimentR/importMothur.R
+ Source: R/importMothur.R
importMothur.RdTreeSummarizedExperimentR/importQIIME2.R
+ Source: R/importQIIME2.R
importQIIME2.RdTreeSummarizedExperimentR/importTaxpasta.R
+ Source: R/importTaxpasta.R
importTaxpasta.RdSummarizedExperiment object into a long data.frameR/meltAssay.R
+ Source: R/meltAssay.R
meltSE.RdmeltSE Converts a
-SummarizedExperiment
-object into a long data.frame which can be used for tidyverse-tools.
SummarizedExperiment object into a
+long data.frame which can be used for tidyverse-tools.
meltSE(x, ...)
+ meltSE(
+ x,
+ assay.type = assay_name,
+ assay_name = "counts",
+ add.row = add_row_data,
+ add_row_data = NULL,
+ add.col = add_col_data,
+ add_col_data = NULL,
+ row.name = feature_name,
+ feature_name = "FeatureID",
+ col.name = sample_name,
+ sample_name = "SampleID",
+ ...
+)
# S4 method for class 'SummarizedExperiment'
meltSE(
@@ -84,14 +97,6 @@ Arguments
...
-optional arguments:
check.names: Logical scalar. Passed to data.frame
-function's check.name argument. Determines if sample names are checked
-that they are syntactically valid variable names and are not duplicated.
-If they are not, sample names are modified. (Default: TRUE)
assay.type
Character scalar. Specifies which assay to use for
calculation. (Default: "counts")
Arguments
If add.row = NULL no data will be added, if
add.row = TRUE all data will be added and if
add.row is a character vector, it will be used to subset
-to given column names in rowData. (Default: NULL)
+to given column names in rowData. (Default:
+NULL)
add_row_data
@@ -115,10 +121,10 @@ Arguments
add.col
-Logical scalar. NULL, or
-character vector. Used to select information from the colData
-to add to the molten assay data. If add.col = NULL no data will
-be added, if add.col = TRUE all data will be added and if
+
Logical scalar. NULL ,or character vector. Used to
+select information from the colData to add to the molten assay data.
+If add.col = NULL no data will be added, if
+add.col = TRUE all data will be added and if
add.col is a character vector, it will be used to subset
to given column names in colData. (Default: NULL)
Arguments
sample_name
Deprecated. Use col.name instead.
...
+optional arguments:
check_names: Logical scalar. Passed to data.frame function's check.name
+argument. Determines if sample names are checked that they are syntactically
+valid variable names and are not duplicated. If they are not, sample names
+are modified. (Default: TRUE)
Value
A tibble with the molten data. The assay values are given in a
column named like the selected assay assay.type. In addition, a
column “FeatureID” will contain the rownames, if set, and analogously
-a column “SampleID” with the colnames, if set.
+a column “SampleID” with the colnames, if set
Details
@@ -163,12 +177,11 @@ Details
Examples
data(GlobalPatterns)
-molten_tse <- meltSE(
- GlobalPatterns,
- assay.type = "counts",
- add.row = TRUE,
- add.col = TRUE
- )
+molten_tse <- meltSE(GlobalPatterns,
+ assay.type = "counts",
+ add.row = TRUE,
+ add.col = TRUE
+ )
molten_tse
#> # A tibble: 499,616 × 17
#> FeatureID SampleID counts Kingdom Phylum Class Order Family Genus Species
diff --git a/reference/mergeSEs.html b/reference/mergeSEs.html
index 933480531..0f28980d3 100644
--- a/reference/mergeSEs.html
+++ b/reference/mergeSEs.html
@@ -17,7 +17,7 @@
@@ -44,7 +44,7 @@
diff --git a/reference/mia-datasets.html b/reference/mia-datasets.html
index fd7529110..aebad58db 100644
--- a/reference/mia-datasets.html
+++ b/reference/mia-datasets.html
@@ -20,7 +20,7 @@
@@ -47,7 +47,7 @@
diff --git a/reference/mia-package.html b/reference/mia-package.html
index 66adfd76c..09cf8f9f8 100644
--- a/reference/mia-package.html
+++ b/reference/mia-package.html
@@ -22,7 +22,7 @@
@@ -49,7 +49,7 @@
diff --git a/reference/peerj13075.html b/reference/peerj13075.html
index a95cbab4f..3db1b889c 100644
--- a/reference/peerj13075.html
+++ b/reference/peerj13075.html
@@ -22,7 +22,7 @@
@@ -49,7 +49,7 @@
diff --git a/reference/rarefyAssay.html b/reference/rarefyAssay.html
index f3b5a556d..fcb8691f2 100644
--- a/reference/rarefyAssay.html
+++ b/reference/rarefyAssay.html
@@ -20,7 +20,7 @@
@@ -47,7 +47,7 @@
diff --git a/reference/runCCA-2.png b/reference/runCCA-2.png
index 4edd0c762..3c8ceddb7 100644
Binary files a/reference/runCCA-2.png and b/reference/runCCA-2.png differ
diff --git a/reference/runCCA.html b/reference/runCCA.html
index b6dde99dd..f29485f26 100644
--- a/reference/runCCA.html
+++ b/reference/runCCA.html
@@ -18,7 +18,7 @@
@@ -45,7 +45,7 @@
Canonical Correspondence Analysis and Redundancy Analysis
- Source: R/runCCA.R
+ Source: R/runCCA.R
runCCA.Rd
diff --git a/reference/runDPCoA.html b/reference/runDPCoA.html
index 5e25aba74..25f30c1eb 100644
--- a/reference/runDPCoA.html
+++ b/reference/runDPCoA.html
@@ -19,7 +19,7 @@
@@ -46,7 +46,7 @@
Calculation of Double Principal Correspondance analysis
- Source: R/runDPCoA.R
+ Source: R/runDPCoA.R
runDPCoA.Rd
diff --git a/reference/runNMDS.html b/reference/runNMDS.html
index e3f14915b..e46496477 100644
--- a/reference/runNMDS.html
+++ b/reference/runNMDS.html
@@ -18,7 +18,7 @@
@@ -45,7 +45,7 @@
diff --git a/reference/splitOn.html b/reference/splitOn.html
index 148513ee0..e491ecfe2 100644
--- a/reference/splitOn.html
+++ b/reference/splitOn.html
@@ -18,7 +18,7 @@
@@ -45,7 +45,7 @@
Split TreeSummarizedExperiment column-wise or row-wise based on grouping variable
- Source: R/splitOn.R
+ Source: R/splitOn.R
splitOn.Rd
@@ -222,7 +222,7 @@ Examples
#> assays(1): counts
#> rownames(19216): 549322 522457 ... 200359 271582
#> rowData names(8): Kingdom Phylum ... Species group
-#> colnames(26): CL3 M11Fcsw ... NP2 TS28
+#> colnames(26): CL3 CC1 ... Even2 Even3
#> colData names(8): X.SampleID Primer ... Description group
#> reducedDimNames(0):
#> mainExpName: NULL
diff --git a/reference/summaries.html b/reference/summaries.html
index 046c2a661..6e1141b87 100644
--- a/reference/summaries.html
+++ b/reference/summaries.html
@@ -18,7 +18,7 @@
@@ -45,7 +45,7 @@
diff --git a/reference/taxonomy-methods.html b/reference/taxonomy-methods.html
index e5814cfd2..f55dba631 100644
--- a/reference/taxonomy-methods.html
+++ b/reference/taxonomy-methods.html
@@ -19,7 +19,7 @@
@@ -46,7 +46,7 @@
Functions for accessing taxonomic data stored in rowData.
- Source: R/taxonomy.R
+ Source: R/taxonomy.R
taxonomy-methods.Rd
diff --git a/reference/transformAssay.html b/reference/transformAssay.html
index b9f4eb306..7e838bfff 100644
--- a/reference/transformAssay.html
+++ b/reference/transformAssay.html
@@ -18,7 +18,7 @@
@@ -45,7 +45,7 @@