Function reference
-
read_adat()
read.adat()
is.soma_adat()
- Read (Load) SomaLogic ADATs
-
write_adat()
- Write an ADAT to File
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print(<soma_adat>)
summary(<soma_adat>)
`[`(<soma_adat>)
`$`(<soma_adat>)
`[[`(<soma_adat>)
`[<-`(<soma_adat>)
`$<-`(<soma_adat>)
`[[<-`(<soma_adat>)
median(<soma_adat>)
- The
soma_adat
Class and S3 Methods
-
loadAdatsAsList()
collapseAdats()
- Load ADAT files as a list
-
parseHeader()
- SomaLogic ADAT parser
-
Col.Meta
colmeta
annotations
rowmeta
- Analyte Annotations, Col.Meta, and Row Info
-
is_intact_attr()
is.intact.attributes()
- Are Attributes Intact?
-
Math(<soma_adat>)
antilog()
Ops(<soma_adat>)
Summary(<soma_adat>)
`==`(<soma_adat>)
- Group Generics for
soma_adat
Class Objects
-
reexports
count
rename
slice_sample
slice
sample_frac
sample_n
filter
mutate
arrange
group_by
ungroup
left_join
anti_join
full_join
inner_join
semi_join
right_join
unite
separate
- Objects exported from other packages
-
getSeqId()
regexSeqId()
locateSeqId()
seqid2apt()
apt2seqid()
is.apt()
is.SeqId()
matchSeqIds()
getSeqIdMatches()
- Working with SomaLogic SeqIds
-
is_seqFormat()
- Test
AptName
Format
-
getAnalyteInfo()
getTargetNames()
getFeatureData()
- Get Analyte Annotation Information
-
getAnalytes()
getMeta()
getFeatures()
- Get Analytes
-
diffAdats()
- Diff Two ADAT Objects
-
merge_clin()
- Merge Clinical Data into SomaScan
Transform Between SomaScan Versions
Functionality required to bridge between SomaScan versions, e.g. 11k -> 7k, sometimes referred to as “lifting”.
-
lift_adat()
is_lifted()
- Lift an ADAT Between Assay Versions
-
read_annotations()
- Import a SomaLogic Annotations File
-
transform(<soma_adat>)
- Scale Transform
soma_adat
Columns/Rows
-
getAdatVersion()
getSomaScanVersion()
getSignalSpace()
checkSomaScanVersion()
getSomaScanLiftCCC()
- Helpers to Extract Information from an ADAT
-
adat2eSet()
- Convert ADAT to ExpressionSet Object
-
pivotExpressionSet()
meltExpressionSet()
- Convert to Long Format
Helpers
Accessor functions to add, modify, or retreive attribute information. Typically used internally but are exported for user convenience.
-
addAttributes()
- Add Attributes to
soma_adat
Objects
-
addClass()
- Add a Class to an Object
-
cleanNames()
- Clean Up Character String
-
getAdatVersion()
getSomaScanVersion()
getSignalSpace()
checkSomaScanVersion()
getSomaScanLiftCCC()
- Helpers to Extract Information from an ADAT
-
SomaScanObjects
example_data
ex_analytes
ex_anno_tbl
ex_target_names
- Example Data and Objects
-
params
- Common Parameters in SomaDataIO
-
SomaDataIO-deprecated
getSomamers
getSomamerData
- Deprecated function(s) of the SomaDataIO package