单倍型出现这种问题，怎么解决

Rscript $scriptsdir/hap_analysis.r -v BnaA01G0307600ZS.recode.vcf -g $datadir/ZS11.v0.gff3 -p $datadir/Sugar2025.txt -G $datadir/group.txt -c scaffoldA01 -s 28774799 -e 28776525

WARNING: ignoring environment value of R_HOME

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Registered S3 method overwritten by 'pegas':

method from

[.haplotype genetics

Attaching package: ‘geneHapR’

The following objects are masked _by_ ‘.GlobalEnv’:

gff, pheno, vcf

Scanning file to determine attributes.

File attributes:

meta lines: 3374

header_line: 3375

variant count: 5

column count: 279

Meta line 3374 read in.

All meta lines processed.

gt matrix initialized.

Character matrix gt created.

Character matrix gt rows: 5

Character matrix gt cols: 279

skip: 0

nrows: 5

row_num: 0

Processed variant: 5

All variants processed

Extracting gt element GT

Error in plotHapTable(hapSummary, hapPrefix = hapPrefix, angle = 45, displayIndelSize = 0, :

please check 'hapSummary' and 'hapPrefix'

Execution halted

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默认排序时间排序

2 个回答

Ti Amo 1天前

hapSummary或 hapPrefix参数有问题，导致无法正确提取或匹配单倍型结果。
我们脚本里会自动给hapPrefix赋值为“Hap”，所以应该是hapSummary出现了问题。
hapSummary是对hapResult进行汇总整理得到的，通过你上面的这个log文件：

Scanning file to determine attributes.

File attributes:

meta lines: 3374

header_line: 3375

variant count: 5

column count: 279

Meta line 3374 read in.

All meta lines processed.

gt matrix initialized.

Character matrix gt created.

Character matrix gt rows: 5

Character matrix gt cols: 279

skip: 0

nrows: 5

row_num: 0

Processed variant: 5

All variants processed

279个样本在这个区间里面5个位点，后面出现一个row_num: 0 表示经过过滤后，没有任何一个变异位点被保留下来。
如果在这五个位点里面所有位点都存在杂合/缺失样本，那就删完了。
可以选择自己修改脚本73和74行，不要过率

不如 15小时前

# 从VCF开始单倍型鉴定

hapResult <- vcf2hap(vcf, hapPrefix = hapPrefix,

hetero_remove = TRUE, # 移除包含杂合位点的样本

na_drop = TRUE) # 移除包含基因型缺失的样本

就是把这段代码注释掉，不运行是吗

单倍型出现这种问题，怎么解决

2 个回答

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