parsing the output of qiime2出错
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parsing the output of qiime2
otuqzafile <- system.file("extdata", "table.qza", package="MicrobiotaProcess")
taxaqzafile <- system.file("extdata", "taxa.qza", package="MicrobiotaProcess")
mapfile <- system.file("extdata", "metadata_qza.txt", package="MicrobiotaProcess")
mpse2 <- mp_import_qiime2(otuqza=otuqzafile, taxaqza=taxaqzafile, mapfilename=mapfile)
mpse2
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
! # Invaild edge matrix for . A <tbl_df> is returned.
ℹ invalid tbl_tree object. Missing column: parent,node.
ℹ invalid tbl_tree object. Missing column: parent,node,label.
! # Invaild edge matrix for . A <tbl_df> is returned.
A MPSE-tibble (MPSE object) abstraction: 12,006 × 32
OTU=138 | Samples=87 | Assays=Abundance | Taxonomy=Kingdom, Phylum, Class, Order, Family, Genus, Speies
OTU Sample Abundance Sample_Name_s BarcodeSequence LinkerPrimerSequence Subject Sex Age Pittsburgh
1 OTU_1 ERR1331… 901 LR53 AGTGTCGATTCG TATGGTAATTGT Patient Male 63 2
2 OTU_2 ERR1331… 877 LR53 AGTGTCGATTCG TATGGTAATTGT Patient Male 63 2
3 OTU_3 ERR1331… 239 LR53 AGTGTCGATTCG TATGGTAATTGT Patient Male 63 2
4 OTU_4 ERR1331… 201 LR53 AGTGTCGATTCG TATGGTAATTGT Patient Male 63 2
5 OTU_5 ERR1331… 168 LR53 AGTGTCGATTCG TATGGTAATTGT Patient Male 63 2
6 OTU_6 ERR1331… 115 LR53 AGTGTCGATTCG TATGGTAATTGT Patient Male 63 2
7 OTU_7 ERR1331… 107 LR53 AGTGTCGATTCG TATGGTAATTGT Patient Male 63 2
8 OTU_8 ERR1331… 84 LR53 AGTGTCGATTCG TATGGTAATTGT Patient Male 63 2
9 OTU_9 ERR1331… 67 LR53 AGTGTCGATTCG TATGGTAATTGT Patient Male 63 2
10 OTU_10 ERR1331… 67 LR53 AGTGTCGATTCG TATGGTAATTGT Patient Male 63 2
ℹ 11,996 more rows
ℹ 22 more variables: Bell , BMI , sCD14ugml , LBPugml , LPSpgml , IFABPpgml ,
Physical_functioning , Role_physical , Role_emotional , Energy_fatigue ,
Emotional_well_being , Social_functioning , Pain , General_health ,
Description , Kingdom , Phylum , Class , Order , Family , Genus ,
Speies
ℹ Use print(n = ...) to see more rows
你好，我分别用了两种方法安装，使用了官方的示例数据，但每次都会报错nvalid tbl_tree object. Missing column: parent.和Invaild edge matrix for . A <tbl_df> is returned.，请问是哪儿出了问题呢？谢谢。
这个不是报错信息，是MicrobiotaProcess调用的tidytree，tidytree内部的提醒信息，可以用remotes::install_github('YuLab-SMU/MicrobiotaProcess')下载开发版，或者用options(check.tbl_tree.verbose = FALSE)就可以屏蔽这些信息