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Cluster record

Source: R/all-classes.R
ClstrRec-class.Rd

Cluster record contains all information on a cluster.

Usage

# S4 method for class 'ClstrRec'
as.character(x)

# S4 method for class 'ClstrRec'
show(object)

# S4 method for class 'ClstrRec'
print(x)

# S4 method for class 'ClstrRec'
str(object, max.level = 2L, ...)

# S4 method for class 'ClstrRec'
summary(object)

Arguments

x

ClstrRec object

object

ClstrRec object

max.level

Maximum level of nesting for str()

...

Further arguments for str()

Slots

id

Cluster ID, integer

sids

Sequence IDs

nsqs

Number of sequences

txids

Source txids for sequences

ntx

Number of taxa

typ

Cluster type: direct, subtree or merged

seed

Seed sequence ID

prnt

Parent taxonomic ID

See also

Other run-public: ClstrArc-class, Phylota-class, SeqArc-class, SeqRec-class, TaxDict-class, TaxRec-class, clusters2_run(), clusters_run(), parameters_reset(), reset(), restart(), run(), setup(), taxise_run()

Examples

data('aotus')
clstrrec <- aotus@clstrs@clstrs[[1]]
# this is a ClstrRec object
# it contains cluster information
show(clstrrec)
#> Cluster Record [id 0]
#>  - [subtree] type
#>  - [AF129795.1] seed sequence
#>  - [173] sequences
#>  - [5] taxa
# you can access its different data slots with @
clstrrec@id     # cluster id
#> [1] 0
clstrrec@sids   # sequence IDs
#>   [1] "AF129792.1" "AF129793.1" "AF129794.1" "AF129795.1" "AF129796.1"
#>   [6] "AF129797.1" "AF129798.1" "AF129799.1" "AF129800.1" "AF129801.1"
#>  [11] "AF129802.1" "AF129803.1" "AF129804.1" "AF129805.1" "AF129806.1"
#>  [16] "AF129807.1" "AF129808.1" "AF132755.1" "AF132756.1" "AF132757.1"
#>  [21] "AF132758.1" "AF132759.1" "AF132760.1" "AF132761.1" "AF132762.1"
#>  [26] "AF132763.1" "AF132764.1" "AF132765.1" "AF132766.1" "AF132767.1"
#>  [31] "AF132768.1" "AF132769.1" "AF132770.1" "AF169485.1" "AF169486.1"
#>  [36] "AF169487.1" "AY227055.1" "AY227056.1" "AY227057.1" "AY227058.1"
#>  [41] "AY227059.1" "AY227060.1" "AY227061.1" "AY227062.1" "AY227063.1"
#>  [46] "AY227064.1" "AY227065.1" "AY227066.1" "AY227067.1" "AY227068.1"
#>  [51] "AY227069.1" "AY227070.1" "AY227071.1" "AY227072.1" "AY227073.1"
#>  [56] "AY227074.1" "AY429142.1" "AY429143.1" "AY493661.1" "AY563180.2"
#>  [61] "AY563181.2" "AY563182.2" "AY563183.2" "AY563184.2" "AY563185.2"
#>  [66] "AY563186.2" "AY563188.2" "AY563189.2" "AY563190.2" "AY563191.2"
#>  [71] "AY563192.2" "AY563193.2" "AY563194.2" "AY563195.2" "AY563196.2"
#>  [76] "AY563197.2" "AY563198.2" "AY563199.2" "AY563200.2" "AY563201.2"
#>  [81] "AY563202.2" "AY563203.2" "AY563204.2" "AY563206.2" "AY563207.2"
#>  [86] "AY563208.2" "AY563209.2" "AY563210.2" "AY563211.2" "AY563212.2"
#>  [91] "AY563213.2" "AY563214.2" "AY563215.2" "AY563216.2" "AY563217.2"
#>  [96] "AY563218.2" "AY563219.2" "AY563220.2" "AY563221.2" "AY563222.2"
#> [101] "AY563223.2" "AY563224.2" "AY563225.2" "AY563226.2" "AY563227.2"
#> [106] "AY563228.2" "AY563229.2" "AY563230.2" "AY563231.2" "AY563232.2"
#> [111] "AY563233.2" "AY563234.2" "AY563236.2" "AY563237.2" "AY563239.2"
#> [116] "AY563241.2" "AY563242.2" "AY563243.2" "AY563244.2" "AY563245.2"
#> [121] "AY563246.2" "AY563247.2" "AY563248.2" "AY563249.2" "AY563250.2"
#> [126] "AY563251.2" "AY563252.2" "AY563253.2" "AY563254.2" "AY563255.2"
#> [131] "AY563256.2" "AY563257.2" "AY563258.2" "AY563259.2" "AY563260.2"
#> [136] "AY563261.2" "AY563262.2" "AY563263.2" "DQ162624.1" "DQ162626.1"
#> [141] "DQ162627.1" "DQ162628.1" "DQ162629.1" "DQ162630.1" "DQ162633.1"
#> [146] "DQ162634.1" "DQ162635.1" "DQ162645.1" "DQ162646.1" "DQ162647.1"
#> [151] "DQ162648.1" "DQ162660.1" "DQ162661.1" "DQ162668.1" "DQ162676.1"
#> [156] "DQ162679.1" "DQ162682.1" "DQ162683.1" "DQ162688.1" "DQ162699.1"
#> [161] "DQ162704.1" "DQ162705.1" "DQ162710.1" "DQ162711.1" "DQ162718.1"
#> [166] "DQ162719.1" "DQ162727.1" "DQ162729.1" "DQ162732.1" "DQ162736.1"
#> [171] "MF615382.1" "MF615383.1" "MF615384.1"
clstrrec@nsqs   # number of sequences
#> [1] 173
clstrrec@txids  # taxonomic IDs of sequences
#>   [1] "231953" "231953" "231953" "231953" "231953" "231953" "231953" "231953"
#>   [9] "231953" "231953" "231953" "231953" "231953" "231953" "231953" "231953"
#>  [17] "231953" "231953" "231953" "231953" "57176"  "57176"  "57176"  "57176" 
#>  [25] "57176"  "57176"  "57176"  "57176"  "57176"  "57176"  "57176"  "57176" 
#>  [33] "57176"  "57175"  "57175"  "57175"  "57175"  "57175"  "57175"  "57175" 
#>  [41] "57175"  "57175"  "57175"  "57175"  "57175"  "57175"  "57175"  "57175" 
#>  [49] "57175"  "57175"  "57175"  "57175"  "57175"  "57175"  "57175"  "57175" 
#>  [57] "57175"  "57175"  "57175"  "57175"  "57175"  "57175"  "57175"  "57175" 
#>  [65] "57175"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#>  [73] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#>  [81] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#>  [89] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#>  [97] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#> [105] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#> [113] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#> [121] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#> [129] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#> [137] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#> [145] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#> [153] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#> [161] "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293"  "37293" 
#> [169] "37293"  "37293"  "37293"  "30591"  "30591" 
clstrrec@ntx    # number unique taxonomic IDs
#> [1] 5
clstrrec@typ    # cluster type: merged, subtree, direct or paraphyly
#> [1] "subtree"
clstrrec@prnt   # MRCA of all taxa
#> [1] "9504"
clstrrec@seed   # most inter-connected sequence
#> [1] "AF129795.1"