g1000_eur.genes.out即为gene-based 关联分析结果: gene-based 关联分析结果的释义如下所示: • GENE: the gene ID as specified in the annotation file • CHR: the chromosome the gene is on • START/STOP: the annotation boundaries of the gene on that chromosome (this includes any window arou...
magma --bfile /GWAS/split_chr/Middle/chr1 --gene-annot gevin.genes.annot --out gevin_gene_based_rawdata 基于SNP p-value数据的基因分析 magma --bfile /GWAS/split_chr/Middle/chr1 --gene-annot gevin.genes.annot --pval SNPassocFisher.result use=2,8 N=170 --out gevin_gene_based 参数分别...
The gene analysis in MAGMA is based on a multiple linear principal components regression [18] model, using an F-test to compute the gene p-value. This model first projects the SNP matrix for a gene onto its principal components (PC), pruning away PCs with very small eigenvalues, and then...
MAGMA——做gene analysis的GWAS数据分析软件 2020-10-24 21:54 −... 桃花换小鱼干好不好 0 7275 Python Ethical Hacking - TROJANS Analysis(3) 2019-10-13 16:13 −BYPASSING ANTI-VIRUS PROGRAMS AV programs detect viruses based on: 1. Code - compare files to huge databases of signatures. -...
4.2 step2: gene-based 关联分析 输入命令: magma --bfile g1000_eur --pval snpp N=401670 --gene-annot g1000_eur.genes.annot --out genebased g1000_eur文件通过前面的第二个步骤获得; snpp文件通过前面的第三个步骤获得; g1000_eur.genes.annot文件通过 4.1 步骤获得; ...
下面简要介绍基于 MAGMA 的 gene-based 关联分析研究。 1. 下载、安装 MAGMA wget https://ctg.cncr.nl/software/MAGMA/prog/magma_v1.09.zip unzip magma_v1.09.zip 2. 下载公共数据 # 下载基因位置文件NCBI37.3.gene.locwget https://ctg.cncr.nl/software/MAGMA/aux_files/NCBI37.3.zip unzipNCBI37.3....
MAGMA在基因集分析中有了很大功能提升。其中：MAGMA软件输入数据既可以是原始数据也可以是关联分析结果数据，既可以进行gene-based分析挖掘特定表型相关的基因，也可以进行生物通路水平的分析，在充分使用测序数据和表型的同时也丰富了我们的分析结果。https://ctg.cncr.nl/software/magma ...
基于GWAS的分析结果做基因集富集分析。 基本代码: 1 2 3 4 5 6 7 8 9 10 11 12 # download sumstats file from https://ctg.cncr.nl/software/summary_statistics # download NCBI37 and g1000_eur from https://ctg.cncr.nl/software/magma ...