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2024-03-12

2024-03-12

作者: 程凉皮儿 | 来源:发表于2024-03-11 12:51 被阅读0次

    TwosampleMR

    Liangping Cheng

    12 三月, 2024

    学习使用TwosampleMR

    首先是安装必要的包,有的网络是打不开github的所以需要魔法帮忙下载,下载好了之后就能在自己的目录下安装了。

    #install.packages("devtools")
    #devtools::install_local("TwoSampleMR-master.zip")
    #devtools::install_local("MRInstruments-master.zip")
    

    加载R包,获取数据

    You can also embed plots, for example:

    ## TwoSampleMR version 0.5.10 
    ## [>] New: Option to use non-European LD reference panels for clumping etc
    ## [>] Some studies temporarily quarantined to verify effect allele
    ## [>] See news(package='TwoSampleMR') and https://gwas.mrcieu.ac.uk for further details
    
    ## API: public: http://gwas-api.mrcieu.ac.uk/
    
    ## OpenGWAS updates:
    
    ##   Date: 2024-03-07
    
    ##   [>] There is exceptional load on the OpenGWAS servers.
    
    ##   [>] Urgent infrastructure development being performed.
    
    ##   [>] The servers will be unavailable for approximately 48 hrs.
    
    ##   [>] See other options for analysis: https://mrcieu.github.io/gwasvcf/.
    
    ## Extracting data for 65 SNP(s) from 1 GWAS(s)
    
    ## Harmonising Cheese intake || id:ukb-b-1489 (ukb-b-1489) and Coronary heart disease || id:ieu-a-7 (ieu-a-7)
    
    ## Removing the following SNPs for being palindromic with intermediate allele frequencies:
    ## rs1024853, rs26579
    
    ## Analysing 'ukb-b-1489' on 'ieu-a-7'
    
    ##   id.exposure id.outcome                              outcome
    ## 1  ukb-b-1489    ieu-a-7 Coronary heart disease || id:ieu-a-7
    ## 2  ukb-b-1489    ieu-a-7 Coronary heart disease || id:ieu-a-7
    ## 3  ukb-b-1489    ieu-a-7 Coronary heart disease || id:ieu-a-7
    ## 4  ukb-b-1489    ieu-a-7 Coronary heart disease || id:ieu-a-7
    ## 5  ukb-b-1489    ieu-a-7 Coronary heart disease || id:ieu-a-7
    ##                         exposure                    method nsnp          b
    ## 1 Cheese intake || id:ukb-b-1489                  MR Egger   62  0.1342111
    ## 2 Cheese intake || id:ukb-b-1489           Weighted median   62 -0.4300205
    ## 3 Cheese intake || id:ukb-b-1489 Inverse variance weighted   62 -0.4360602
    ## 4 Cheese intake || id:ukb-b-1489               Simple mode   62 -0.5269452
    ## 5 Cheese intake || id:ukb-b-1489             Weighted mode   62 -0.4311161
    ##          se         pval
    ## 1 0.4309722 7.565649e-01
    ## 2 0.1306445 9.964392e-04
    ## 3 0.1022658 2.008084e-05
    ## 4 0.3037105 8.778662e-02
    ## 5 0.2724922 1.187931e-01
    
    ##   id.exposure id.outcome                              outcome
    ## 1  ukb-b-1489    ieu-a-7 Coronary heart disease || id:ieu-a-7
    ## 2  ukb-b-1489    ieu-a-7 Coronary heart disease || id:ieu-a-7
    ##                         exposure                    method        Q Q_df
    ## 1 Cheese intake || id:ukb-b-1489                  MR Egger 81.96134   60
    ## 2 Cheese intake || id:ukb-b-1489 Inverse variance weighted 84.49375   61
    ##       Q_pval
    ## 1 0.03135632
    ## 2 0.02492620
    
    ## Analysing 'ukb-b-1489' on 'ieu-a-7'
    
    ##   id.exposure id.outcome                              outcome
    ## 1  ukb-b-1489    ieu-a-7 Coronary heart disease || id:ieu-a-7
    ##                         exposure
    ## 1 Cheese intake || id:ukb-b-1489
    ##                                                      method nsnp          b
    ## 1 Inverse variance weighted (multiplicative random effects)   62 -0.4360602
    ##          se         pval
    ## 1 0.1022658 2.008084e-05
    
    ##   id.exposure id.outcome                              outcome
    ## 1  ukb-b-1489    ieu-a-7 Coronary heart disease || id:ieu-a-7
    ##                         exposure egger_intercept          se      pval
    ## 1 Cheese intake || id:ukb-b-1489    -0.009837988 0.007225505 0.1784265
    
    ## $`ukb-b-1489.ieu-a-7`
    
    ## Warning: Using linewidth for a discrete variable is not advised.
    
    ## Warning: Removed 1 row containing missing values or values outside the scale range
    ## (`geom_errorbarh()`).
    
    ## Warning: Removed 1 row containing missing values or values outside the scale range
    ## (`geom_point()`).
    
    image.png
    ## 
    ## attr(,"split_type")
    ## [1] "data.frame"
    ## attr(,"split_labels")
    ##   id.exposure id.outcome
    ## 1  ukb-b-1489    ieu-a-7
    
    ## $`ukb-b-1489.ieu-a-7`
    
    image.png
    ## 
    ## attr(,"split_type")
    ## [1] "data.frame"
    ## attr(,"split_labels")
    ##   id.exposure id.outcome
    ## 1  ukb-b-1489    ieu-a-7
    
    ## $`ukb-b-1489.ieu-a-7`
    
    ## Warning: Removed 1 row containing missing values or values outside the scale range
    ## (`geom_errorbarh()`).
    ## Removed 1 row containing missing values or values outside the scale range
    ## (`geom_point()`).
    
    image.png
    ## 
    ## attr(,"split_type")
    ## [1] "data.frame"
    ## attr(,"split_labels")
    ##   id.exposure id.outcome
    ## 1  ukb-b-1489    ieu-a-7
    
    ## $`ukb-b-1489.ieu-a-7`
    
    image.png
    ## 
    ## attr(,"split_type")
    ## [1] "data.frame"
    ## attr(,"split_labels")
    ##   id.exposure id.outcome
    ## 1  ukb-b-1489    ieu-a-7
    

    Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

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