Description Usage Arguments Details Value See Also Examples
Plot the observed SNP p-values for each gene
1 | plot_genes(obs.outfile, gene.list, op=NULL)
|
obs.outfile |
The output file of observed p-values from |
gene.list |
See |
op |
List of options. See |
If the option gene.list$chrm.var
is not specified, then it is assumed that all the SNPs
are on the same chromosome, and the same color will be used in the plot. If gene.list$chrm.var
is specified, then the genes will be grouped by chromosome with the same color for the group.
Options list:
Below are the names for the options list op
.
cex.axis
See par
colors
Colors to use for each gene in the plot
maxLabelLen
Maximum length of x-axis labels
chr.text
See par
x.las
See par
x.padj
See par
A data frame containing the SNP ids, parameter estimates, genes, etc.
1 2 3 4 5 6 7 8 9 10 | # Get the file of observed p-values
obs_file <- system.file("sampleData", "obs_pvalues.txt", package="ARTP")
# Define the gene-SNP list
gs_file <- system.file("sampleData", "gene_SNP_data.txt", package="ARTP")
gene.list <- list(file=gs_file, delimiter="\t", header=1,
snp.var="SNP", gene.var="Gene")
plot_genes(obs_file, gene.list)
|
Read 50 items
Read 50 items
Read 50 items
Read 50 items
Read 50 items
Read 1 item
SNP Pvalue Pvalue.flag Beta SE
1 rs111546 0.09693691 0 -0.179885542868972 0.108372071990276
2 rs679512 0.6959555 0 0.0424054621059663 0.108513279339869
3 rs601084 0.2376595 0 0.130574112501498 0.110575713543273
4 rs711504 0.1424374 0 -0.157562376845515 0.107420998765337
5 rs677636 0.6163505 0 -0.0564105950922082 0.112589422964676
6 rs776914 0.0618205 0 0.206241603441257 0.110432481773471
7 rs707881 0.343469 0 0.10490973280384 0.110742174457283
8 rs045071 0.5166842 0 0.0733082063091525 0.113048816792798
9 rs023502 0.3054294 0 -0.115258866373855 0.112463060534928
10 rs350111 0.5981452 0 0.0587057581775082 0.111381395975208
11 rs943580 0.8260588 0 -0.0240753369637776 0.109553323055287
12 rs710834 0.2465002 0 -0.126787477407513 0.109404053331235
13 rs873041 0.8555399 0 0.0204846038026022 0.112519050214399
14 rs907292 0.5165383 0 -0.0719122341169303 0.11085750492301
15 rs869720 0.002133421 0 -0.343052931886046 0.111707185375106
16 rs845434 0.3518095 0 -0.102501533049523 0.110088242931839
17 rs970602 0.03126954 0 0.245310568892198 0.113905852198469
18 rs467442 0.6382245 0 0.0513930178081695 0.10930434721052
19 rs568502 0.3567487 0 0.0992820704477744 0.10773049835635
20 rs789349 0.2417197 0 -0.129713738635107 0.11080021528614
21 rs483698 0.9002325 0 0.013705287582751 0.109320728149567
22 rs257422 0.2385562 0 -0.129467719586668 0.109848422643348
23 rs304539 0.6014501 0 -0.0583726872871319 0.111757350138933
24 rs540465 0.5075491 0 -0.0728492706016712 0.109934814664446
25 rs460053 0.0148385 0 0.269233494181084 0.110509307433127
26 rs090634 0.527107 0 -0.0694200174928294 0.109767402032607
27 rs902453 0.4280208 0 0.0887486738020001 0.111973983897237
28 rs556112 0.002111349 0 -0.341155990695376 0.110977326806018
29 rs651810 0.9602076 0 -0.00541145406641567 0.108461020249305
30 rs081827 0.3463527 0 -0.102177323381279 0.108504511242214
31 rs657122 0.7304196 0 0.0383139666478865 0.111194396224046
32 rs523523 0.4405566 0 -0.0835555004735847 0.108337242456089
33 rs247716 0.5769716 0 0.0639152657523113 0.114581736784783
34 rs732255 0.03917095 0 -0.23185238226432 0.112419461242631
35 rs013720 0.8195503 0 -0.0250624730402308 0.109863640775804
36 rs274103 0.6024686 0 0.0579641641631473 0.111286829723024
37 rs693822 0.1791079 0 -0.149147566803175 0.111013633078906
38 rs269238 0.3135151 0 0.108501520357496 0.10765388970792
39 rs115265 0.8596696 0 0.0192417111356911 0.10883645061282
40 rs254030 0.6953693 0 0.0419884503940435 0.10722854597832
41 rs683489 0.7243595 0 -0.038118149549605 0.108094152723342
42 rs262589 0.7752592 0 -0.0306663897601796 0.107411972360338
43 rs975021 0.7418598 0 0.0354946602720176 0.107758286677054
44 rs342947 0.01052636 0 0.288454434916937 0.112763786575373
45 rs265436 0.7589576 0 -0.0335118914181365 0.109212649205729
46 rs817723 0.625559 0 0.0534721806133871 0.109577033423779
47 rs859372 0.4186917 0 0.0903124577502524 0.111677036714732
48 rs014342 0.1049309 0 0.176453459052182 0.108827518684439
49 rs620579 0.3089676 0 -0.111854851817797 0.10994285984358
50 rs711571 0.4376787 0 0.0867483836075134 0.111771997410273
OR CI Gene
1 0.8353658 (0.6755, 1.0331) Gene_4
2 1.0433174 (0.8434, 1.2906) Gene_4
3 1.1394824 (0.9175, 1.4152) Gene_1
4 0.8542235 (0.692, 1.0544) Gene_2
5 0.9451510 (0.758, 1.1785) Gene_2
6 1.2290501 (0.9898, 1.5261) Gene_2
7 1.1106104 (0.8939, 1.3798) Gene_4
8 1.0760621 (0.8622, 1.343) Gene_3
9 0.8911354 (0.7148, 1.1109) Gene_3
10 1.0604632 (0.8525, 1.3192) Gene_3
11 0.9762122 (0.7876, 1.21) Gene_3
12 0.8809209 (0.7109, 1.0916) Gene_1
13 1.0206959 (0.8187, 1.2725) Gene_1
14 0.9306126 (0.7489, 1.1565) Gene_3
15 0.7096007 (0.5701, 0.8833) Gene_4
16 0.9025768 (0.7274, 1.1199) Gene_3
17 1.2780182 (1.0223, 1.5977) Gene_4
18 1.0527366 (0.8497, 1.3043) Gene_3
19 1.1043778 (0.8942, 1.364) Gene_3
20 0.8783468 (0.7069, 1.0914) Gene_4
21 1.0137996 (0.8183, 1.2561) Gene_1
22 0.8785629 (0.7084, 1.0896) Gene_2
23 0.9432983 (0.7577, 1.1743) Gene_4
24 0.9297410 (0.7495, 1.1533) Gene_3
25 1.3089607 (1.054, 1.6255) Gene_1
26 0.9329347 (0.7523, 1.1569) Gene_4
27 1.0928060 (0.8775, 1.361) Gene_3
28 0.7109480 (0.572, 0.8837) Gene_1
29 0.9946032 (0.8041, 1.2302) Gene_1
30 0.9028694 (0.7299, 1.1168) Gene_3
31 1.0390574 (0.8356, 1.2921) Gene_3
32 0.9198400 (0.7439, 1.1374) Gene_4
33 1.0660021 (0.8516, 1.3344) Gene_3
34 0.7930632 (0.6362, 0.9886) Gene_4
35 0.9752490 (0.7863, 1.2096) Gene_2
36 1.0596770 (0.852, 1.318) Gene_3
37 0.8614420 (0.693, 1.0708) Gene_3
38 1.1146066 (0.9026, 1.3764) Gene_1
39 1.0194280 (0.8236, 1.2618) Gene_4
40 1.0428824 (0.8452, 1.2868) Gene_1
41 0.9625992 (0.7788, 1.1898) Gene_3
42 0.9697991 (0.7857, 1.1971) Gene_2
43 1.0361321 (0.8389, 1.2798) Gene_2
44 1.3343635 (1.0698, 1.6644) Gene_2
45 0.9670434 (0.7807, 1.1979) Gene_4
46 1.0549276 (0.851, 1.3077) Gene_2
47 1.0945162 (0.8793, 1.3623) Gene_2
48 1.1929789 (0.9638, 1.4766) Gene_2
49 0.8941740 (0.7208, 1.1092) Gene_2
50 1.0906222 (0.8761, 1.3577) Gene_3
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