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Write summary of phyter analysis to file(s)

Source: R/write.phylter.R
write.phylter.Rd

Write the summary of the phylter analysis in a txt file or as a pdf report.

Usage

write.phylter(
  x,
  file = "",
  include.discarded = TRUE,
  pdfreport = FALSE,
  pdfreport.file = "report.pdf"
)

Arguments

x

The object returned by the 'phylter()' function.

file

Name of the file where to write the text summary of the phylter output. If "" (the default), write.phylyer() prints to the standard output.

include.discarded

Logical. If TRUE (the default) the elements discarded before the analysis are still in the list of Outliers in the output. Useful for cleaning datasets after a phylter analysis.

pdfreport

Logical. Should a full report of the phylter analysis

pdfreport.file

If report=TRUE, name of the pdf file where the report is written. Default to report.pdf

Value

No return value

Examples

data(carnivora) 
res <- phylter(carnivora, parallel = FALSE)
#> 
#> Number of Genes:    125
#> Number of Species:  53
#> --------
#> Initial score: 0.86235
#>     28  new cells to remove -> New score: 0.90272 -> OK
#>     18  new cells to remove -> New score: 0.90833 -> OK
#>     16  new cells to remove -> New score: 0.91501 -> OK
#>     18  new cells to remove -> New score: 0.92561 -> OK
#>     5  new cells to remove -> New score: 0.93404 -> OK
#>     4  new cells to remove -> New score: 0.93692 -> OK
#>     2  new cells to remove -> New score: 0.93712 -> OK
#>     1  new cells to remove -> New score: 0.94392 -> OK
#>     1  new cells to remove -> New score: 0.94417 -> OK
#>     1  new cells to remove -> New score: 0.94426 -> OK
#>  => No more outliers detected  ->  Checking for complete gene outliers
#>  => No more outliers detected  ->  STOPPING OPTIMIZATION
#> --------
#> 
#> Total number of outliers detected: 94
#>   Number of complete gene outliers : 0
#>   Number of complete species outliers : 0
#> 
#> Gain (concordance between matrices): 8.19% 
#> Loss (data filtering): 1.42% 
# write a full report to the standard output
write.phylter(res) 
#> # 
#> # -- phylter v. 0.9.12 -- 
#> # Thu Jul 25 13:51:59 2024
#> # 
#> # 
#> # 
#> # PARAMETERS
#> # 
#> # bvalue=0
#> # distance=patristic
#> # k=3
#> # k2=3
#> # Norm=median
#> # Norm.cutoff=0.001
#> # test.island=TRUE
#> # verbose=TRUE
#> # stop.criteria=1e-05
#> # InitialOnly=FALSE
#> # normalizeby=row
#> # 
#> # CLEANING STEP
#> # 
#> # Initial number of genes passed to phylter: 125
#> # Number of genes discarded before the analysis: 0
#> # Genes discarded: 
#> # 
#> # SUMMARY
#> # 
#> # Number of genes analyzed: 125
#> # Number of species analyzed: 53
#> # Total number of outliers detected: 94
#> # Number of complete gene outliers : 0
#> # Number of complete species outliers : 0
#> # Initial score of the compromise: 0.862353534028201
#> # Final score of the compromise: 0.944259987303489
#> # Gain: 8.19% 
#> # Loss (data filtering): 1.42% 
#> # 
#> # OUTLIERS (including discarded elements, if any)
#> # 
#> # Genes	Species
#> ENSG00000005381_MPO	Arctocephalus_gazella
#> ENSG00000005381_MPO	Ursus_maritimus
#> ENSG00000005381_MPO	Ailurus_fulgens
#> ENSG00000106511_MEOX2	Panthera_tigris
#> ENSG00000106511_MEOX2	Mustela_putorius
#> ENSG00000114686_MRPL3	Procyon_lotor
#> ENSG00000116157_GPX7	Vulpes_vulpes
#> ENSG00000116761_CTH	Otocyon_megalotis
#> ENSG00000120053_GOT1	Phoca_vitulina
#> ENSG00000120053_GOT1	Gulo_gulo
#> ENSG00000123307_NEUROD4	Arctocephalus_gazella
#> ENSG00000132254_ARFIP2	Panthera_leo
#> ENSG00000132254_ARFIP2	Odobenus_rosmarus
#> ENSG00000132254_ARFIP2	Felis_catus
#> ENSG00000132254_ARFIP2	Arctocephalus_gazella
#> ENSG00000132693_CRP	Hyaena_hyaena
#> ENSG00000132693_CRP	Pteronura_brasiliensis
#> ENSG00000132693_CRP	Neovison_vison
#> ENSG00000132693_CRP	Eumetopias_jubatus
#> ENSG00000133135_RNF128	Cryptoprocta_ferox
#> ENSG00000133135_RNF128	Panthera_tigris
#> ENSG00000133135_RNF128	Phoca_vitulina
#> ENSG00000134240_HMGCS2	Gulo_gulo
#> ENSG00000134240_HMGCS2	Spilogale_gracilis
#> ENSG00000138675_FGF5	Taxidea_taxus
#> ENSG00000138675_FGF5	Lutra_lutra
#> ENSG00000143125_PROK1	Potos_flavus
#> ENSG00000149573_MPZL2	Paradoxurus_hermaphroditus
#> ENSG00000073111_MCM2	Paradoxurus_hermaphroditus
#> ENSG00000106511_MEOX2	Manis_javanica
#> ENSG00000106511_MEOX2	Acinonyx_jubatus
#> ENSG00000106511_MEOX2	Panthera_pardus
#> ENSG00000106511_MEOX2	Leptonychotes_weddellii
#> ENSG00000114686_MRPL3	Arctocephalus_gazella
#> ENSG00000116157_GPX7	Canis_familiaris
#> ENSG00000116157_GPX7	Otocyon_megalotis
#> ENSG00000116761_CTH	Vulpes_vulpes
#> ENSG00000132693_CRP	Enhydra_lutris
#> ENSG00000132693_CRP	Crocuta_Crocuta
#> ENSG00000132693_CRP	Arctocephalus_gazella
#> ENSG00000132693_CRP	Zalophus_californianus
#> ENSG00000133135_RNF128	Ursus_americanus
#> ENSG00000138675_FGF5	Mustela_putorius
#> ENSG00000138675_FGF5	Mellivora_capensis
#> ENSG00000143125_PROK1	Paradoxurus_hermaphroditus
#> ENSG00000149573_MPZL2	Mungos_mungo
#> ENSG00000106511_MEOX2	Panthera_onca
#> ENSG00000106511_MEOX2	Felis_catus
#> ENSG00000106511_MEOX2	Enhydra_lutris
#> ENSG00000106511_MEOX2	Ailuropoda_melanoleuca
#> ENSG00000106511_MEOX2	Odobenus_rosmarus
#> ENSG00000106511_MEOX2	Paradoxurus_hermaphroditus
#> ENSG00000106511_MEOX2	Neofelis_nebulosa
#> ENSG00000114686_MRPL3	Taxidea_taxus
#> ENSG00000116157_GPX7	Lycaon_pictus
#> ENSG00000132693_CRP	Lutra_lutra
#> ENSG00000133135_RNF128	Procyon_lotor
#> ENSG00000138675_FGF5	Enhydra_lutris
#> ENSG00000143125_PROK1	Nasua_narica
#> ENSG00000144355_DLX1	Acinonyx_jubatus
#> ENSG00000149573_MPZL2	Suricata_suricatta
#> ENSG00000149573_MPZL2	Helogale_parvula
#> ENSG00000106511_MEOX2	Lynx_pardinus
#> ENSG00000106511_MEOX2	Gulo_gulo
#> ENSG00000106511_MEOX2	Ursus_maritimus
#> ENSG00000106511_MEOX2	Eumetopias_jubatus
#> ENSG00000106511_MEOX2	Neomonachus_schauinslandi
#> ENSG00000106511_MEOX2	Potos_flavus
#> ENSG00000106511_MEOX2	Panthera_leo
#> ENSG00000106511_MEOX2	Prionailurus_bengalensis
#> ENSG00000106511_MEOX2	Canis_familiaris
#> ENSG00000106511_MEOX2	Neovison_vison
#> ENSG00000114686_MRPL3	Pteronura_brasiliensis
#> ENSG00000116761_CTH	Canis_familiaris
#> ENSG00000133135_RNF128	Mellivora_capensis
#> ENSG00000133135_RNF128	Acinonyx_jubatus
#> ENSG00000138675_FGF5	Gulo_gulo
#> ENSG00000138675_FGF5	Neovison_vison
#> ENSG00000143125_PROK1	Gulo_gulo
#> ENSG00000149573_MPZL2	Cryptoprocta_ferox
#> ENSG00000106511_MEOX2	Lynx_canadensis
#> ENSG00000106511_MEOX2	Zalophus_californianus
#> ENSG00000106511_MEOX2	Mirounga_angustirostris
#> ENSG00000133135_RNF128	Pteronura_brasiliensis
#> ENSG00000143125_PROK1	Otocyon_megalotis
#> ENSG00000106511_MEOX2	Puma_concolor
#> ENSG00000106511_MEOX2	Callorhinus_ursinus
#> ENSG00000143125_PROK1	Vulpes_vulpes
#> ENSG00000143196_DPT	Ailurus_fulgens
#> ENSG00000138675_FGF5	Pteronura_brasiliensis
#> ENSG00000143125_PROK1	Lycaon_pictus
#> ENSG00000143125_PROK1	Manis_javanica
#> ENSG00000116761_CTH	Lycaon_pictus
#> ENSG00000143196_DPT	Taxidea_taxus