PRSice中的家庭$linkfun（mustart）错误
我试图使用PRSice计算多基因风险分数，但错误不断发生：PRSice中的家庭$linkfun（mustart）错误,r,R,我试图使用PRSice计算多基因风险分数，但错误不断发生： Error in family$linkfun(mustart) : Argument mu must be a nonempty numeric vector Calls: process_plot ... glm -> eval -> eval -> glm.fit -> <Anonymous> -> .Call 如果您在任何已出版作品中使用PRSice，请引用： Jack Euesd
Error in family$linkfun(mustart) :
Argument mu must be a nonempty numeric vector
Calls: process_plot ... glm -> eval -> eval -> glm.fit -> <Anonymous> -> .Call
2020-09-18 12:51:06
/usr/local/software/bioinformatics/prsice/PRSice \
--A1 effect_allele \
--A2 other_allele \
--bar-levels 0.001000,0.050000,0.100000,0.200000,0.300000,0.400000,0.500000,1.000000 \
--base sumstas.final.noamb.nodup.final.gz \
--beta \
--binary-target T \
--bp base_pair_location \
--clump-kb 250 \
--clump-p 1.000000 \
--clump-r2 0.100000 \
--cov-file target.cov \
--info-base INFO,0.9 \
--interval 0.000050 \
--lower 0.000100 \
--model add \
--out Results.case.control \
--pheno-file pheno.portuguese.prs.txt \
--pvalue p_value \
--seed 183062393 \
--snp variant_id \
--stat beta \
--target Results \
--thread 1 \
--upper 0.500000
Loading Genotype file: Results (bed)
878 people (562 male(s), 316 female(s)) observed
878 founder(s) included
772439 ambiguous variant(s) excluded
4311463 variant(s) included
1 region included
Start processing sumstas.final.noamb.nodup.final
Due to library restrictions, we cannot display progress bar
for gz
Reading 100.00%
Base file: sumstas.final.noamb.nodup.final.gz
GZ file detected. Header of file is:
chromosome base_pair_location variant_id effect_allele other_allele beta standard_error p_value
7112757 variant(s) observed in base file, with:
4790987 variant(s) not found in target file
2321770 total variant(s) included from base file
Start performing clumping
128891 MB RAM detected; reserving 1 MB for clumping
Clumping Progress: 100.00%
Number of variant(s) after clumping : 114973
Check Phenotype file: pheno.portuguese.prs.txt
Column Name of Sample ID: FID+IID
Note: If the phenotype file does not contain a header, the
column name will be displayed as the Sample ID which is ok.
Phenotype Name: pheno
There are a total of 1 phenotype to process
623 control(s)
255 case(s)
9 valid covariates included
Processing the covariate file: target.cov
After reading the covariate file, 878 sample(s) included in
the analysis
Processing 100.00%
There are 1 region(s) with p-value between 0.1 and 1e-5
(may not be significant); Please note that these
results are inflated due to the overfitting inherent in
finding the best-fit PRS (but it's still best to find the
best-fit PRS!).
You can use the --perm option (see manual) to calculate an
empirical P-value.
Error in family$linkfun(mustart) :
Argument mu must be a nonempty numeric vector
Calls: process_plot ... glm -> eval -> eval -> glm.fit -> <Anonymous> -> .Call
In addition: Warning message:
In max(pheno$Pheno) : no non-missing arguments to max; returning -Inf
2020-09-1812:51:06
/usr/本地/软件/生物信息学/prsice/prsice\
--A1效应等位基因\
--A2其他_等位基因\
--钢筋等级0.001000,0.050000,0.100000,0.200000,0.300000,0.400000,0.500000,1.000000\
--基本集水坑.final.noamb.nodup.final.gz\
--贝塔\
--二元目标T\
--bp碱基对位置\
--束kb 250\
--clump-p 1.000000\
--clump-r2 0.100000\
--cov文件target.cov\
--信息基础信息，0.9\
--区间0.000050\
--低于0.000100\
--模型添加\
--结果、病例、对照\
--pheno文件pheno.葡萄牙语.prs.txt\
--p值p_值\
--种子183062393\
--snp变体\
--统计β\
--目标结果\
--线程1\
--上限0.500000
加载基因型文件：结果（bed）
观察到878人（562名男性，316名女性）
包括878名创始人
772439不包括不明确的变体
包括4311463个变体
包括1个区域
开始处理sumstas.final.noamb.nodup.final
由于库限制，我们无法显示进度条
广州
读数100.00%
基本文件：sumstas.final.noamb.nodup.final.gz
检测到GZ文件。文件头是：
染色体碱基对位置变异id效应等位基因其他等位基因β标准错误p值
7112757基本文件中观察到的变体，包括：
在目标文件中找不到4790987变体
基本文件中包含的变量总数为2321770
开始执行聚集
检测到128891 MB内存；保留1 MB用于聚集
成束进度：100.00%
聚集后的变体数：114973
检查表型文件：pheno.葡萄牙语.prs.txt
样本ID的列名：FID+IID
注意：如果显型文件不包含头，则
列名将显示为样本ID，这是正常的。
表型名称：表型
总共有1个表型需要处理
623管制
255宗
包括9个有效的协变量
处理协变量文件：target.cov
阅读协变量文件后，878个样本包括在
分析
处理100.00%
有1个区域的p值介于0.1和1e-5之间
（可能不重要）；请注意这些
由于中固有的过度拟合，结果被夸大
找到最合适的PRS（但最好还是找到
最合适的PRS！）。
可以使用--perm选项（请参阅手册）计算
经验P值。
家庭$linkfun（mustart）中存在错误：
参数mu必须是非空的数值向量
调用：进程\u绘图。。。glm->eval->eval->glm.fit->->->。呼叫
此外：警告信息：
在max中（pheno$pheno）：max没有不丢失的参数；返回-Inf
2020-09-18 12:51:06
/usr/local/software/bioinformatics/prsice/PRSice \
--A1 effect_allele \
--A2 other_allele \
--bar-levels 0.001000,0.050000,0.100000,0.200000,0.300000,0.400000,0.500000,1.000000 \
--base sumstas.final.noamb.nodup.final.gz \
--beta \
--binary-target T \
--bp base_pair_location \
--clump-kb 250 \
--clump-p 1.000000 \
--clump-r2 0.100000 \
--cov-file target.cov \
--info-base INFO,0.9 \
--interval 0.000050 \
--lower 0.000100 \
--model add \
--out Results.case.control \
--pheno-file pheno.portuguese.prs.txt \
--pvalue p_value \
--seed 183062393 \
--snp variant_id \
--stat beta \
--target Results \
--thread 1 \
--upper 0.500000
Loading Genotype file: Results (bed)
878 people (562 male(s), 316 female(s)) observed
878 founder(s) included
772439 ambiguous variant(s) excluded
4311463 variant(s) included
1 region included
Start processing sumstas.final.noamb.nodup.final
Due to library restrictions, we cannot display progress bar
for gz
Reading 100.00%
Base file: sumstas.final.noamb.nodup.final.gz
GZ file detected. Header of file is:
chromosome base_pair_location variant_id effect_allele other_allele beta standard_error p_value
7112757 variant(s) observed in base file, with:
4790987 variant(s) not found in target file
2321770 total variant(s) included from base file
Start performing clumping
128891 MB RAM detected; reserving 1 MB for clumping
Clumping Progress: 100.00%
Number of variant(s) after clumping : 114973
Check Phenotype file: pheno.portuguese.prs.txt
Column Name of Sample ID: FID+IID
Note: If the phenotype file does not contain a header, the
column name will be displayed as the Sample ID which is ok.
Phenotype Name: pheno
There are a total of 1 phenotype to process
623 control(s)
255 case(s)
9 valid covariates included
Processing the covariate file: target.cov
After reading the covariate file, 878 sample(s) included in
the analysis
Processing 100.00%
There are 1 region(s) with p-value between 0.1 and 1e-5
(may not be significant); Please note that these
results are inflated due to the overfitting inherent in
finding the best-fit PRS (but it's still best to find the
best-fit PRS!).
You can use the --perm option (see manual) to calculate an
empirical P-value.
Error in family$linkfun(mustart) :
Argument mu must be a nonempty numeric vector
Calls: process_plot ... glm -> eval -> eval -> glm.fit -> <Anonymous> -> .Call
In addition: Warning message:
In max(pheno$Pheno) : no non-missing arguments to max; returning -Inf