基因关联分析 Gene-based analysis 第二部,进行基于基因的关联分析, 示例代码如下所示: magma \ --bfile [REFDATA] \ --pval [PVAL_FILE] \ N=[N] \ --gene-annot [ANNOT_PREFIX].genes.annot \ --out [GENE_PREFIX] bfile为原始数据或是参考LD面板,如果数据量不大可以直接使用自己的plink的bed格式原...
• N: the sample size used when analysing that gene; can differ for allosomal chromosomes or when analysing SNP p-value input with variable sample size by SNP (due to missingness or differences in coverage in meta-analysis) • ZSTAT: the Z-value for the gene, based on its (permutatio...
随着接触复杂疾病相关研究,经常会查询相关文献,而MAGMA(Multi-marker Analysis of GenoMic Annotation)在高分文献中高频出现。 MAGMA包括三个功能模块: ①注释步骤,将SNP map到基因中; ②基于基因关联分析,计算基于基因和性状的关联显著性,在这又可以分为两个部分,一种是基于raw data的gene-based关联分析,另一种是基...
• N: the sample size used when analysing that gene; can differ for allosomal chromosomes or when analysing SNP p-value input with variable sample size by SNP (due to missingness or differences in coverage in meta-analysis) • ZSTAT: the Z-value for the gene, based on its (permutatio...
• N: the sample size used when analysing that gene; can differ for allosomal chromosomes or when analysing SNP p-value input with variable sample size by SNP (due to missingness or differences in coverage in meta-analysis) • ZSTAT: the Z-value for the gene, based on its (permutatio...
MAGMA软件第一步是SNP注释步骤，输入的文件是bim文件（plink格式文件）和基因的位置信息。 magma --annotate --snp-loc [SNPLOC_FILE] --gene-loc [GENELOC_FILE] --out [OUTPUT_PREFIX] ①SNP位置信息文件应该包含三列，即前三列为SNP ID, chromosome, 和base pair position，如果是plink...
2# ever Smoking_TAG数据进行Gene-based analysis: nohup ./magma --bfile g1000_eur --pval ./GWAS_Summary_SCZ_Smoking/ever_smoking.results_Pval N=69409 --gene-annot ever_smoking_SNP_Gene_annotation.genes.annot --out ever_smoking_SNP_Gene_Analysis_P & ...
2# ever Smoking_TAG数据进行Gene-based analysis: nohup ./magma --bfile g1000_eur --pval ./GWAS_Summary_SCZ_Smoking/ever_smoking.results_Pval N=69409 --gene-annot ever_smoking_SNP_Gene_annotation.genes.annot --out ever_smoking_SNP_Gene_Analysis_P & ...
# Gene-set analysis ../magma--gene-resultstest.gene.genes.raw --set-annot geneSet/formated.msigdb.v7.2.entrez.gmt --out GS_test Annotation的结果 就是把SNP的ID归到了gene里,NCBI (Entrez) Gene IDs 1 2 3 4 5 6 7 8 9 10 11
2# ever Smoking_TAG数据进行Gene-based analysis: nohup ./magma --bfile g1000_eur --pval ./GWAS_Summary_SCZ_Smoking/ever_smoking.results_Pval N=69409 --gene-annot ever_smoking_SNP_Gene_annotation.genes.annot --out ever_smoking_SNP_Gene_Analysis_P & ...