简易的Msigdb数据包
2020-10-31 本文已影响0人
一只烟酒僧
参考连接：https://www.jianshu.com/p/f2febb3123d8
一、安装
BiocManager::install("msigdbr")
二、简单使用
msigdbr_species()
# A tibble: 11 x 2
species_name species_common_name
<chr> <chr>
1 Bos taurus cattle
2 Caenorhabditis elegans roundworm
3 Canis lupus familiaris dog
4 Danio rerio zebrafish
5 Drosophila melanogaster fruit fly
6 Gallus gallus chicken
7 Homo sapiens human
8 Mus musculus house mouse
9 Rattus norvegicus Norway rat
10 Saccharomyces cerevisiae baker's or brewer's yeast
11 Sus scrofa pig
hallmarker<-msigdbr(species = "Mus musculus",category = "H")
# A tibble: 7,309 x 17
gs_cat gs_subcat gs_name entrez_gene gene_symbol human_entrez_ge… human_gene_symb… gs_id gs_pmid gs_geoid gs_exact_source
<chr> <chr> <chr> <int> <chr> <int> <chr> <chr> <chr> <chr> <chr>
1 H "" HALLMA… 11303 Abca1 19 ABCA1 M5905 "" "" ""
2 H "" HALLMA… 74610 Abcb8 11194 ABCB8 M5905 "" "" ""
3 H "" HALLMA… 52538 Acaa2 10449 ACAA2 M5905 "" "" ""
4 H "" HALLMA… 11363 Acadl 33 ACADL M5905 "" "" ""
5 H "" HALLMA… 11364 Acadm 34 ACADM M5905 "" "" ""
6 H "" HALLMA… 11409 Acads 35 ACADS M5905 "" "" ""
7 H "" HALLMA… 104112 Acly 47 ACLY M5905 "" "" ""
8 H "" HALLMA… 11429 Aco2 50 ACO2 M5905 "" "" ""
9 H "" HALLMA… 11430 Acox1 51 ACOX1 M5905 "" "" ""
10 H "" HALLMA… 11512 Adcy6 112 ADCY6 M5905 "" "" ""
# … with 7,299 more rows, and 6 more variables: gs_url <chr>, gs_description <chr>, species_name <chr>,
# species_common_name <chr>, ortholog_sources <chr>, num_ortholog_sources <dbl>
C1<-msigdbr(category = "C1")
gs_cat gs_subcat gs_name entrez_gene gene_symbol human_entrez_ge… human_gene_symb… gs_id gs_pmid gs_geoid gs_exact_source
<chr> <chr> <chr> <int> <chr> <int> <chr> <chr> <chr> <chr> <chr>
1 C1 "" chr10p… 26983 ABCD1P2 26983 ABCD1P2 M183… "" "" ""
2 C1 "" chr10p… 399746 ACTR3BP5 399746 ACTR3BP5 M183… "" "" ""
3 C1 "" chr10p… 100288319 AK3P5 100288319 AK3P5 M183… "" "" ""
4 C1 "" chr10p… 100420618 AL117339.4 100420618 AL117339.4 M183… "" "" ""
5 C1 "" chr10p… 91074 ANKRD30A 91074 ANKRD30A M183… "" "" ""
6 C1 "" chr10p… 94134 ARHGAP12 94134 ARHGAP12 M183… "" "" ""
7 C1 "" chr10p… 646348 ARL6IP1P2 646348 ARL6IP1P2 M183… "" "" ""
8 C1 "" chr10p… 100462843 ATP6V1G1P4 100462843 ATP6V1G1P4 M183… "" "" ""
9 C1 "" chr10p… 554049 C1DP1 554049 C1DP1 M183… "" "" ""
10 C1 "" chr10p… 79741 CCDC7 79741 CCDC7 M183… "" "" ""
# … with 40,046 more rows, and 6 more variables: gs_url <chr>, gs_description <chr>, species_name <chr>,
# species_common_name <chr>, ortholog_sources <chr>, num_ortholog_sources <dbl>
三、富集分析
m_t2g = m_df %>% dplyr::select(gs_name, entrez_gene) %>% as.data.frame()
enricher(gene = gene_ids_vector, TERM2GENE = m_t2g, ...)
