diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 2687641d..eba5a55b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -57,6 +57,12 @@ jobs: website coverage + - name: Install blas/lapack + run: | + La_library() + extSoftVersion()["BLAS"] + shell: Rscript {0} + - name: Install reticulate run: | library("reticulate") diff --git a/DESCRIPTION b/DESCRIPTION index 5517bdbb..29593462 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: netZooR Type: Package Title: Unified methods for the inference and analysis of gene regulatory networks -Version: 1.1.14 +Version: 1.1.15 Date: 2022-07-07 Authors@R: c(person("Marouen", "Ben Guebila", email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")), diff --git a/inst/extdata/chip.txt b/inst/extdata/chip.txt deleted file mode 100644 index 623f339e..00000000 --- a/inst/extdata/chip.txt +++ /dev/null @@ -1,6517 +0,0 @@ -"Rv0022c" "Rv0029" 1 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1 -"Rv0678" "Rv3140" 1 -"Rv0678" "Rv3142c" 1 -"Rv0678" "Rv3143" 1 -"Rv0678" "Rv3158" 1 -"Rv0678" "Rv3160c" 1 -"Rv0678" "Rv3196" 1 -"Rv0678" "Rv3216" 1 -"Rv0678" "Rv3219" 1 -"Rv0678" "Rv3240c" 1 -"Rv0678" "Rv3248c" 1 -"Rv0678" "Rv3249c" 1 -"Rv0678" "Rv3250c" 1 -"Rv0678" "Rv3253c" 1 -"Rv0678" "Rv3254" 1 -"Rv0678" "Rv3273" 1 -"Rv0678" "Rv3274c" 1 -"Rv0678" "Rv3275c" 1 -"Rv0678" "Rv3276c" 1 -"Rv0678" "Rv3285" 1 -"Rv0678" "Rv3299c" 1 -"Rv0678" "Rv3300c" 1 -"Rv0678" "Rv3335c" 1 -"Rv0678" "Rv3346c" 1 -"Rv0678" "Rv3353c" 1 -"Rv0678" "Rv3354" 1 -"Rv0678" "Rv3388" 1 -"Rv0678" "Rv3410c" 1 -"Rv0678" "Rv3489" 1 -"Rv0678" "Rv3503c" 1 -"Rv0678" "Rv3504" 1 -"Rv0678" "Rv3527" 1 -"Rv0678" "Rv3539" 1 -"Rv0678" "Rv3597c" 1 -"Rv0678" "Rv3601c" 1 -"Rv0678" "Rv3660c" 1 -"Rv0678" "Rv3661" 1 -"Rv0678" "Rv3674c" 1 -"Rv0678" "Rv3675" 1 -"Rv0678" "Rv3676" 1 -"Rv0678" "Rv3681c" 1 -"Rv0678" "Rv3714c" 1 -"Rv0678" "Rv3716c" 1 -"Rv0678" "Rv3717" 1 -"Rv0678" "Rv3728" 1 -"Rv0678" "Rv3734c" 1 -"Rv0678" "Rv3738c" 1 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"Rv2526" 1 -"Rv0767c" "Rv2638" 1 -"Rv0767c" "Rv3197" 1 -"Rv0818" "Rv0252" 1 -"Rv0818" "Rv0501" 1 -"Rv0818" "Rv1542c" 1 -"Rv0818" "Rv1791" 1 -"Rv0818" "Rv3229c" 1 -"Rv0818" "Rv3384c" 1 -"Rv0818" "Rv3385c" 1 -"Rv0818" "Rv0045c" 1 -"Rv0818" "Rv0245" 1 -"Rv0818" "Rv0469" 1 -"Rv0818" "Rv2281" 1 -"Rv0818" "Rv0244c" 1 -"Rv0818" "Rv1322A" 1 -"Rv0818" "Rv1386" 1 -"Rv0818" "Rv3386" 1 -"Rv0827c" "Rv0827c" 1 -"Rv0827c" "Rv0825c" 1 -"Rv0827c" "Rv0826" 1 -"Rv0827c" "Rv3660c" 1 -"Rv0827c" "Rv3661" 1 -"Rv0880" "Rv0475" 1 -"Rv0880" "Rv0667" 1 -"Rv0880" "Rv0691c" 1 -"Rv0880" "Rv0692" 1 -"Rv0880" "Rv0756c" 1 -"Rv0880" "Rv0757" 1 -"Rv0880" "Rv0793" 1 -"Rv0880" "Rv1078" 1 -"Rv0880" "Rv1180" 1 -"Rv0880" "Rv1219c" 1 -"Rv0880" "Rv1388" 1 -"Rv0880" "Rv1392" 1 -"Rv0880" "Rv2173" 1 -"Rv0880" "Rv2188c" 1 -"Rv0880" "Rv3045" 1 -"Rv0880" "Rv3614c" 1 -"Rv0880" "Rv3738c" 1 -"Rv0880" "Rv0726c" 1 -"Rv0880" "Rv2172c" 1 -"Rv0880" "Rv2590" 1 -"Rv0891c" "Rv3460c" 1 -"Rv0891c" "Rv3461c" 1 -"Rv0894" "Rv1795" 1 -"Rv0967" "Rv0967" 1 -"Rv0967" "Rv0034" 1 -"Rv0967" "Rv0050" 1 -"Rv0967" "Rv0116c" 1 -"Rv0967" "Rv0117" 1 -"Rv0967" "Rv0126" 1 -"Rv0967" "Rv0155" 1 -"Rv0967" "Rv0163" 1 -"Rv0967" "Rv0204c" 1 -"Rv0967" "Rv0226c" 1 -"Rv0967" "Rv0271c" 1 -"Rv0967" "Rv0284" 1 -"Rv0967" "Rv0295c" 1 -"Rv0967" "Rv0326" 1 -"Rv0967" "Rv0340" 1 -"Rv0967" "Rv0351" 1 -"Rv0967" "Rv0353" 1 -"Rv0967" "Rv0380c" 1 -"Rv0967" "Rv0399c" 1 -"Rv0967" "Rv0411c" 1 -"Rv0967" "Rv0436c" 1 -"Rv0967" "Rv0448c" 1 -"Rv0967" "Rv0468" 1 -"Rv0967" "Rv0514" 1 -"Rv0967" "Rv0519c" 1 -"Rv0967" "Rv0551c" 1 -"Rv0967" "Rv0552" 1 -"Rv0967" "Rv0574c" 1 -"Rv0967" "Rv0585c" 1 -"Rv0967" "Rv0600c" 1 -"Rv0967" "Rv0615" 1 -"Rv0967" "Rv0651" 1 -"Rv0967" "Rv0713" 1 -"Rv0967" "Rv0714" 1 -"Rv0967" "Rv0727c" 1 -"Rv0967" "Rv0730" 1 -"Rv0967" "Rv0733" 1 -"Rv0967" "Rv0747" 1 -"Rv0967" "Rv0770" 1 -"Rv0967" "Rv0774c" 1 -"Rv0967" "Rv0775" 1 -"Rv0967" "Rv0783c" 1 -"Rv0967" "Rv0810c" 1 -"Rv0967" "Rv0811c" 1 -"Rv0967" "Rv0812" 1 -"Rv0967" "Rv0822c" 1 -"Rv0967" "Rv0830" 1 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"Rv1490" 1 -"Rv0967" "Rv1500" 1 -"Rv0967" "Rv1538c" 1 -"Rv0967" "Rv1539" 1 -"Rv0967" "Rv1614" 1 -"Rv0967" "Rv1624c" 1 -"Rv0967" "Rv1632c" 1 -"Rv0967" "Rv1644" 1 -"Rv0967" "Rv1653" 1 -"Rv0967" "Rv1669" 1 -"Rv0967" "Rv1705c" 1 -"Rv0967" "Rv1706c" 1 -"Rv0967" "Rv1715" 1 -"Rv0967" "Rv1724c" 1 -"Rv0967" "Rv1725c" 1 -"Rv0967" "Rv1726" 1 -"Rv0967" "Rv1729c" 1 -"Rv0967" "Rv1735c" 1 -"Rv0967" "Rv1739c" 1 -"Rv0967" "Rv1740" 1 -"Rv0967" "Rv1741" 1 -"Rv0967" "Rv1743" 1 -"Rv0967" "Rv1747" 1 -"Rv0967" "Rv1765c" 1 -"Rv0967" "Rv1770" 1 -"Rv0967" "Rv1818c" 1 -"Rv0967" "Rv1839c" 1 -"Rv0967" "Rv1841c" 1 -"Rv0967" "Rv1845c" 1 -"Rv0967" "Rv1864c" 1 -"Rv0967" "Rv1876" 1 -"Rv0967" "Rv1886c" 1 -"Rv0967" "Rv1898" 1 -"Rv0967" "Rv1899c" 1 -"Rv0967" "Rv1912c" 1 -"Rv0967" "Rv1918c" 1 -"Rv0967" "Rv1951c" 1 -"Rv0967" "Rv1953" 1 -"Rv0967" "Rv1967" 1 -"Rv0967" "Rv1971" 1 -"Rv0967" "Rv1990A" 1 -"Rv0967" "Rv1992c" 1 -"Rv0967" "Rv2054" 1 -"Rv0967" "Rv2064" 1 -"Rv0967" "Rv2100" 1 -"Rv0967" "Rv2102" 1 -"Rv0967" "Rv2126c" 1 -"Rv0967" "Rv2139" 1 -"Rv0967" "Rv2146c" 1 -"Rv0967" "Rv2151c" 1 -"Rv0967" "Rv2152c" 1 -"Rv0967" "Rv2197c" 1 -"Rv0967" "Rv2198c" 1 -"Rv0967" "Rv2240c" 1 -"Rv0967" "Rv2246" 1 -"Rv0967" "Rv2271" 1 -"Rv0967" "Rv2370c" 1 -"Rv0967" "Rv2388c" 1 -"Rv0967" "Rv2397c" 1 -"Rv0967" "Rv2398c" 1 -"Rv0967" "Rv2401" 1 -"Rv0967" "Rv2441c" 1 -"Rv0967" "Rv2453c" 1 -"Rv0967" "Rv2485c" 1 -"Rv0967" "Rv2490c" 1 -"Rv0967" "Rv2538c" 1 -"Rv0967" "Rv2551c" 1 -"Rv0967" "Rv2556c" 1 -"Rv0967" "Rv2557" 1 -"Rv0967" "Rv2558" 1 -"Rv0967" "Rv2559c" 1 -"Rv0967" "Rv2581c" 1 -"Rv0967" "Rv2582" 1 -"Rv0967" "Rv2598" 1 -"Rv0967" "Rv2638" 1 -"Rv0967" "Rv2667" 1 -"Rv0967" "Rv2668" 1 -"Rv0967" "Rv2705c" 1 -"Rv0967" "Rv2706c" 1 -"Rv0967" "Rv2707" 1 -"Rv0967" "Rv2754c" 1 -"Rv0967" "Rv2799" 1 -"Rv0967" "Rv2843" 1 -"Rv0967" "Rv2844" 1 -"Rv0967" "Rv2922A" 1 -"Rv0967" "Rv2929" 1 -"Rv0967" "Rv2940c" 1 -"Rv0967" "Rv2959c" 1 -"Rv0967" "Rv2960c" 1 -"Rv0967" "Rv2962c" 1 -"Rv0967" "Rv3046c" 1 -"Rv0967" "Rv3079c" 1 -"Rv0967" "Rv3122" 1 -"Rv0967" "Rv3137" 1 -"Rv0967" "Rv3145" 1 -"Rv0967" "Rv3148" 1 -"Rv0967" "Rv3151" 1 -"Rv0967" "Rv3158" 1 -"Rv0967" "Rv3173c" 1 -"Rv0967" "Rv3174" 1 -"Rv0967" "Rv3224B" 1 -"Rv0967" "Rv3225c" 1 -"Rv0967" "Rv3228" 1 -"Rv0967" "Rv3255c" 1 -"Rv0967" "Rv3273" 1 -"Rv0967" "Rv3282" 1 -"Rv0967" "Rv3336c" 1 -"Rv0967" "Rv3337" 1 -"Rv0967" "Rv3338" 1 -"Rv0967" "Rv3340" 1 -"Rv0967" "Rv3355c" 1 -"Rv0967" "Rv3390" 1 -"Rv0967" "Rv3394c" 1 -"Rv0967" "Rv3419c" 1 -"Rv0967" "Rv3420c" 1 -"Rv0967" "Rv3438" 1 -"Rv0967" "Rv3444c" 1 -"Rv0967" "Rv3445c" 1 -"Rv0967" "Rv3458c" 1 -"Rv0967" "Rv3479" 1 -"Rv0967" "Rv3493c" 1 -"Rv0967" "Rv3495c" 1 -"Rv0967" "Rv3496c" 1 -"Rv0967" "Rv3586" 1 -"Rv0967" "Rv3606c" 1 -"Rv0967" "Rv3614c" 1 -"Rv0967" "Rv3615c" 1 -"Rv0967" "Rv3660c" 1 -"Rv0967" "Rv3690" 1 -"Rv0967" "Rv3693" 1 -"Rv0967" "Rv3712" 1 -"Rv0967" "Rv3713" 1 -"Rv0967" "Rv3740c" 1 -"Rv0967" "Rv3769" 1 -"Rv0967" "Rv3777" 1 -"Rv0967" "Rv3778c" 1 -"Rv0967" "Rv3779" 1 -"Rv0967" "Rv3795" 1 -"Rv0967" "Rv3796" 1 -"Rv0967" "Rv3797" 1 -"Rv0967" "Rv3798" 1 -"Rv0967" "Rv3805c" 1 -"Rv0967" "Rv3812" 1 -"Rv0967" "Rv3815c" 1 -"Rv0967" "Rv3829c" 1 -"Rv0967" "Rv3835" 1 -"Rv0967" "Rv3884c" 1 -"Rv0967" "Rv3894c" 1 -"Rv0967" "Rv3915" 1 -"Rv0967" "Rv3919c" 1 -"Rv0967" "Rv0225" 1 -"Rv0967" "Rv0896" 1 -"Rv0967" "Rv1191" 1 -"Rv0967" "Rv1746" 1 -"Rv0967" "Rv2507" 1 -"Rv0967" "Rv3149" 1 -"Rv0967" "Rv3150" 1 -"Rv0981" "Rv0842" 1 -"Rv0981" "Rv1196" 1 -"Rv0981" "Rv2431c" 1 -"Rv0981" "Rv2432c" 1 -"Rv0981" "Rv2639c" 1 -"Rv1019" "Rv3229c" 1 -"Rv1019" "Rv3230c" 1 -"Rv1019" "Rv3573c" 1 -"Rv1019" "Rv3574" 1 -"Rv1033c" "Rv0032" 1 -"Rv1033c" "Rv1033c" 1 -"Rv1033c" "Rv2107" 1 -"Rv1033c" "Rv3588c" 1 -"Rv1033c" "Rv3681c" 1 -"Rv1033c" "Rv0001" 1 -"Rv1033c" "Rv0004" 1 -"Rv1033c" "Rv0020c" 1 -"Rv1033c" "Rv0022c" 1 -"Rv1033c" "Rv0023" 1 -"Rv1033c" "Rv0047c" 1 -"Rv1033c" "Rv0057" 1 -"Rv1033c" "Rv0058" 1 -"Rv1033c" "Rv0077c" 1 -"Rv1033c" "Rv0078" 1 -"Rv1033c" "Rv0103c" 1 -"Rv1033c" "Rv0112" 1 -"Rv1033c" "Rv0113" 1 -"Rv1033c" "Rv0145" 1 -"Rv1033c" "Rv0165c" 1 -"Rv1033c" "Rv0166" 1 -"Rv1033c" "Rv0169" 1 -"Rv1033c" "Rv0170" 1 -"Rv1033c" "Rv0171" 1 -"Rv1033c" "Rv0173" 1 -"Rv1033c" "Rv0174" 1 -"Rv1033c" "Rv0203" 1 -"Rv1033c" "Rv0208c" 1 -"Rv1033c" "Rv0221" 1 -"Rv1033c" "Rv0222" 1 -"Rv1033c" "Rv0229c" 1 -"Rv1033c" "Rv0233" 1 -"Rv1033c" "Rv0239" 1 -"Rv1033c" "Rv0240" 1 -"Rv1033c" "Rv0242c" 1 -"Rv1033c" "Rv0243" 1 -"Rv1033c" "Rv0244c" 1 -"Rv1033c" "Rv0245" 1 -"Rv1033c" "Rv0251c" 1 -"Rv1033c" "Rv0256c" 1 -"Rv1033c" "Rv0257" 1 -"Rv1033c" "Rv0268c" 1 -"Rv1033c" "Rv0323c" 1 -"Rv1033c" "Rv0324" 1 -"Rv1033c" "Rv0327c" 1 -"Rv1033c" "Rv0328" 1 -"Rv1033c" "Rv0331" 1 -"Rv1033c" "Rv0354c" 1 -"Rv1033c" "Rv0363c" 1 -"Rv1033c" "Rv0388c" 1 -"Rv1033c" "Rv0389" 1 -"Rv1033c" "Rv0402c" 1 -"Rv1033c" "Rv0412c" 1 -"Rv1033c" "Rv0413" 1 -"Rv1033c" "Rv0427c" 1 -"Rv1033c" "Rv0456A" 1 -"Rv1033c" "Rv0457c" 1 -"Rv1033c" "Rv0458" 1 -"Rv1033c" "Rv0475" 1 -"Rv1033c" "Rv0485" 1 -"Rv1033c" "Rv0488" 1 -"Rv1033c" "Rv0490" 1 -"Rv1033c" "Rv0500A" 1 -"Rv1033c" "Rv0502" 1 -"Rv1033c" "Rv0509" 1 -"Rv1033c" "Rv0518" 1 -"Rv1033c" "Rv0590" 1 -"Rv1033c" "Rv0636" 1 -"Rv1033c" "Rv0653c" 1 -"Rv1033c" "Rv0654" 1 -"Rv1033c" "Rv0657c" 1 -"Rv1033c" "Rv0685" 1 -"Rv1033c" "Rv0711" 1 -"Rv1033c" "Rv0719" 1 -"Rv1033c" "Rv0753c" 1 -"Rv1033c" "Rv0757" 1 -"Rv1033c" "Rv0789c" 1 -"Rv1033c" "Rv0824c" 1 -"Rv1033c" "Rv0830" 1 -"Rv1033c" "Rv0839" 1 -"Rv1033c" "Rv0985c" 1 -"Rv1033c" "Rv0987" 1 -"Rv1033c" "Rv0989c" 1 -"Rv1033c" "Rv1019" 1 -"Rv1033c" "Rv1048c" 1 -"Rv1033c" "Rv1050" 1 -"Rv1033c" "Rv1102c" 1 -"Rv1033c" "Rv1103c" 1 -"Rv1033c" "Rv1104" 1 -"Rv1033c" "Rv1117" 1 -"Rv1033c" "Rv1159" 1 -"Rv1033c" "Rv1211" 1 -"Rv1033c" "Rv1221" 1 -"Rv1033c" "Rv1230c" 1 -"Rv1033c" "Rv1268c" 1 -"Rv1033c" "Rv1305" 1 -"Rv1033c" "Rv1374c" 1 -"Rv1033c" "Rv1375" 1 -"Rv1033c" "Rv1403c" 1 -"Rv1033c" "Rv1404" 1 -"Rv1033c" "Rv1419" 1 -"Rv1033c" "Rv1459c" 1 -"Rv1033c" "Rv1460" 1 -"Rv1033c" "Rv1477" 1 -"Rv1033c" "Rv1486c" 1 -"Rv1033c" "Rv1487" 1 -"Rv1033c" "Rv1503c" 1 -"Rv1033c" "Rv1509" 1 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"Rv3908" 1 -"Rv3223c" "Rv1471" 1 -"Rv3223c" "Rv1528c" 1 -"Rv3223c" "Rv1875" 1 -"Rv3223c" "Rv2466c" 1 -"Rv3223c" "Rv2467" 1 -"Rv3223c" "Rv2707" 1 -"Rv3223c" "Rv3206c" 1 -"Rv3223c" "Rv3223c" 1 -"Rv3223c" "Rv3350c" 1 -"Rv3223c" "Rv3913" 1 -"Rv3223c" "Rv0667" 1 -"Rv3223c" "Rv1116" 1 -"Rv3223c" "Rv1298" 1 -"Rv3223c" "Rv1299" 1 -"Rv3223c" "Rv2204c" 1 -"Rv3223c" "Rv2205c" 1 -"Rv3223c" "Rv2705c" 1 -"Rv3223c" "Rv2706c" 1 -"Rv3223c" "Rv3224" 1 -"Rv3223c" "Rv0053" 1 -"Rv3246c" "Rv0040c" 1 -"Rv3246c" "Rv0041" 1 -"Rv3246c" "Rv0113" 1 -"Rv3246c" "Rv0116c" 1 -"Rv3246c" "Rv0129c" 1 -"Rv3246c" "Rv0130" 1 -"Rv3246c" "Rv0179c" 1 -"Rv3246c" "Rv0188" 1 -"Rv3246c" "Rv0208c" 1 -"Rv3246c" "Rv0209" 1 -"Rv3246c" "Rv0252" 1 -"Rv3246c" "Rv0309" 1 -"Rv3246c" "Rv0320" 1 -"Rv3246c" "Rv0456A" 1 -"Rv3246c" "Rv0469" 1 -"Rv3246c" "Rv0643c" 1 -"Rv3246c" "Rv0653c" 1 -"Rv3246c" "Rv0654" 1 -"Rv3246c" "Rv0822c" 1 -"Rv3246c" "Rv0950c" 1 -"Rv3246c" "Rv0996" 1 -"Rv3246c" "Rv1004c" 1 -"Rv3246c" "Rv1009" 1 -"Rv3246c" "Rv1089A" 1 -"Rv3246c" "Rv1116" 1 -"Rv3246c" "Rv1158c" 1 -"Rv3246c" "Rv1159" 1 -"Rv3246c" "Rv1169c" 1 -"Rv3246c" "Rv1170" 1 -"Rv3246c" "Rv1268c" 1 -"Rv3246c" "Rv1433" 1 -"Rv3246c" "Rv1469" 1 -"Rv3246c" "Rv1477" 1 -"Rv3246c" "Rv1522c" 1 -"Rv3246c" "Rv1523" 1 -"Rv3246c" "Rv1690" 1 -"Rv3246c" "Rv1754c" 1 -"Rv3246c" "Rv1772" 1 -"Rv3246c" "Rv1791" 1 -"Rv3246c" "Rv1815" 1 -"Rv3246c" "Rv1883c" 1 -"Rv3246c" "Rv1884c" 1 -"Rv3246c" "Rv1886c" 1 -"Rv3246c" "Rv1908c" 1 -"Rv3246c" "Rv1918c" 1 -"Rv3246c" "Rv1987" 1 -"Rv3246c" "Rv2162c" 1 -"Rv3246c" "Rv2243" 1 -"Rv3246c" "Rv2293c" 1 -"Rv3246c" "Rv2352c" 1 -"Rv3246c" "Rv2462c" 1 -"Rv3246c" "Rv2463" 1 -"Rv3246c" "Rv2525c" 1 -"Rv3246c" "Rv2722" 1 -"Rv3246c" "Rv2723" 1 -"Rv3246c" "Rv2758c" 1 -"Rv3246c" "Rv2864c" 1 -"Rv3246c" "Rv2884" 1 -"Rv3246c" "Rv3159c" 1 -"Rv3246c" "Rv3171c" 1 -"Rv3246c" "Rv3241c" 1 -"Rv3246c" "Rv3245c" 1 -"Rv3246c" "Rv3246c" 1 -"Rv3246c" "Rv3276c" 1 -"Rv3246c" "Rv3277" 1 -"Rv3246c" "Rv3354" 1 -"Rv3246c" "Rv3532" 1 -"Rv3246c" "Rv3583c" 1 -"Rv3246c" "Rv3645" 1 -"Rv3246c" "Rv3674c" 1 -"Rv3246c" "Rv3675" 1 -"Rv3246c" "Rv3676" 1 -"Rv3246c" "Rv3681c" 1 -"Rv3246c" "Rv3716c" 1 -"Rv3246c" "Rv3717" 1 -"Rv3246c" "Rv3810" 1 -"Rv3249c" "Rv0032" 1 -"Rv3249c" "Rv0097" 1 -"Rv3249c" "Rv0404" 1 -"Rv3249c" "Rv2107" 1 -"Rv3249c" "Rv2108" 1 -"Rv3249c" "Rv3409c" 1 -"Rv3249c" "Rv3554" 1 -"Rv3249c" "Rv0006" 1 -"Rv3249c" "Rv0039c" 1 -"Rv3249c" "Rv0057" 1 -"Rv3249c" "Rv0095c" 1 -"Rv3249c" "Rv0118c" 1 -"Rv3249c" "Rv0161" 1 -"Rv3249c" "Rv0172" 1 -"Rv3249c" "Rv0239" 1 -"Rv3249c" "Rv0240" 1 -"Rv3249c" "Rv0299" 1 -"Rv3249c" "Rv0327c" 1 -"Rv3249c" "Rv0328" 1 -"Rv3249c" "Rv0348" 1 -"Rv3249c" "Rv0441c" 1 -"Rv3249c" "Rv0454" 1 -"Rv3249c" "Rv0467" 1 -"Rv3249c" "Rv0514" 1 -"Rv3249c" "Rv0634A" 1 -"Rv3249c" "Rv0667" 1 -"Rv3249c" "Rv0678" 1 -"Rv3249c" "Rv0684" 1 -"Rv3249c" "Rv0688" 1 -"Rv3249c" "Rv0723" 1 -"Rv3249c" "Rv0724" 1 -"Rv3249c" "Rv0773c" 1 -"Rv3249c" "Rv0839" 1 -"Rv3249c" "Rv0887c" 1 -"Rv3249c" "Rv0984" 1 -"Rv3249c" "Rv0994" 1 -"Rv3249c" "Rv1079" 1 -"Rv3249c" "Rv1117" 1 -"Rv3249c" "Rv1129c" 1 -"Rv3249c" "Rv1130" 1 -"Rv3249c" "Rv1133c" 1 -"Rv3249c" "Rv1158c" 1 -"Rv3249c" "Rv1159" 1 -"Rv3249c" "Rv1182" 1 -"Rv3249c" "Rv1183" 1 -"Rv3249c" "Rv1194c" 1 -"Rv3249c" "Rv1198" 1 -"Rv3249c" "Rv1229c" 1 -"Rv3249c" "Rv1306" 1 -"Rv3249c" "Rv1339" 1 -"Rv3249c" "Rv1446c" 1 -"Rv3249c" "Rv1454c" 1 -"Rv3249c" "Rv1500" 1 -"Rv3249c" "Rv1503c" 1 -"Rv3249c" "Rv1505c" 1 -"Rv3249c" "Rv1590" 1 -"Rv3249c" "Rv1614" 1 -"Rv3249c" "Rv1646" 1 -"Rv3249c" "Rv1727" 1 -"Rv3249c" "Rv1753c" 1 -"Rv3249c" "Rv1760" 1 -"Rv3249c" "Rv1833c" 1 -"Rv3249c" "Rv1834" 1 -"Rv3249c" "Rv1865c" 1 -"Rv3249c" "Rv1901" 1 -"Rv3249c" "Rv1936" 1 -"Rv3249c" "Rv1989c" 1 -"Rv3249c" "Rv1990c" 1 -"Rv3249c" "Rv2100" 1 -"Rv3249c" "Rv2245" 1 -"Rv3249c" "Rv2346c" 1 -"Rv3249c" "Rv2367c" 1 -"Rv3249c" "Rv2389c" 1 -"Rv3249c" "Rv2468c" 1 -"Rv3249c" "Rv2470" 1 -"Rv3249c" "Rv2524c" 1 -"Rv3249c" "Rv2556c" 1 -"Rv3249c" "Rv2557" 1 -"Rv3249c" "Rv2608" 1 -"Rv3249c" "Rv2644c" 1 -"Rv3249c" "Rv2786c" 1 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-"Rv3405c" "Rv3406" 1 -"Rv3405c" "Rv3616c" 1 -"Rv3414c" "Rv3414c" 1 -"Rv3414c" "Rv2107" 1 -"Rv3416" "Rv0950c" 1 -"Rv3416" "Rv0095c" 1 -"Rv3416" "Rv0219" 1 -"Rv3416" "Rv2136c" 1 -"Rv3416" "Rv2137c" 1 -"Rv3416" "Rv2138" 1 -"Rv3416" "Rv3686c" 1 -"Rv3416" "Rv0167" 1 -"Rv3417c" "Rv3417c" 1 -"Rv3488" "Rv2983" 1 -"Rv3488" "Rv3488" 1 -"Rv3488" "Rv0047c" 1 -"Rv3488" "Rv0164" 1 -"Rv3488" "Rv0217c" 1 -"Rv3488" "Rv0229c" 1 -"Rv3488" "Rv0275c" 1 -"Rv3488" "Rv0276" 1 -"Rv3488" "Rv0300" 1 -"Rv3488" "Rv0337c" 1 -"Rv3488" "Rv0475" 1 -"Rv3488" "Rv0476" 1 -"Rv3488" "Rv0541c" 1 -"Rv3488" "Rv0578c" 1 -"Rv3488" "Rv0579" 1 -"Rv3488" "Rv0597c" 1 -"Rv3488" "Rv0636" 1 -"Rv3488" "Rv0637" 1 -"Rv3488" "Rv0664" 1 -"Rv3488" "Rv0665" 1 -"Rv3488" "Rv0667" 1 -"Rv3488" "Rv0692" 1 -"Rv3488" "Rv0729" 1 -"Rv3488" "Rv0747" 1 -"Rv3488" "Rv0758" 1 -"Rv3488" "Rv0960" 1 -"Rv3488" "Rv0989c" 1 -"Rv3488" "Rv1193" 1 -"Rv3488" "Rv1248c" 1 -"Rv3488" "Rv1481" 1 -"Rv3488" "Rv1638A" 1 -"Rv3488" "Rv1704c" 1 -"Rv3488" "Rv1719" 1 -"Rv3488" "Rv1772" 1 -"Rv3488" "Rv1837c" 1 -"Rv3488" "Rv1871c" 1 -"Rv3488" "Rv1908c" 1 -"Rv3488" "Rv1963c" 1 -"Rv3488" "Rv1980c" 1 -"Rv3488" "Rv1987" 1 -"Rv3488" "Rv1995" 1 -"Rv3488" "Rv1999c" 1 -"Rv3488" "Rv2000" 1 -"Rv3488" "Rv2058c" 1 -"Rv3488" "Rv2059" 1 -"Rv3488" "Rv2187" 1 -"Rv3488" "Rv2220" 1 -"Rv3488" "Rv2296" 1 -"Rv3488" "Rv2323c" 1 -"Rv3488" "Rv2335" 1 -"Rv3488" "Rv2349c" 1 -"Rv3488" "Rv2399c" 1 -"Rv3488" "Rv2488c" 1 -"Rv3488" "Rv2566" 1 -"Rv3488" "Rv2567" 1 -"Rv3488" "Rv2643" 1 -"Rv3488" "Rv2644c" 1 -"Rv3488" "Rv2703" 1 -"Rv3488" "Rv2719c" 1 -"Rv3488" "Rv2779c" 1 -"Rv3488" "Rv2780" 1 -"Rv3488" "Rv2797c" 1 -"Rv3488" "Rv2931" 1 -"Rv3488" "Rv3017c" 1 -"Rv3488" "Rv3019c" 1 -"Rv3488" "Rv3028c" 1 -"Rv3488" "Rv3101c" 1 -"Rv3488" "Rv3111" 1 -"Rv3488" "Rv3212" 1 -"Rv3488" "Rv3252c" 1 -"Rv3488" "Rv3269" 1 -"Rv3488" "Rv3279c" 1 -"Rv3488" "Rv3363c" 1 -"Rv3488" "Rv3414c" 1 -"Rv3488" "Rv3429" 1 -"Rv3488" "Rv3462c" 1 -"Rv3488" "Rv3477" 1 -"Rv3488" "Rv3486" 1 -"Rv3488" "Rv3539" 1 -"Rv3488" "Rv3738c" 1 -"Rv3488" "Rv3746c" 1 -"Rv3488" "Rv3747" 1 -"Rv3488" "Rv3804c" 1 -"Rv3488" "Rv3810" 1 -"Rv3488" "Rv3811" 1 -"Rv3488" "Rv3832c" 1 -"Rv3488" "Rv3833" 1 -"Rv3488" "Rv3869" 1 -"Rv3488" "Rv3881c" 1 -"Rv3488" "Rv3894c" 1 -"Rv3488" "Rv3919c" 1 -"Rv3488" "Rv0154c" 1 -"Rv3488" "Rv1952" 1 -"Rv3488" "Rv2343c" 1 -"Rv3557c" "Rv0793" 1 -"Rv3557c" "Rv0320" 1 -"Rv3557c" "Rv1572c" 1 -"Rv3557c" "Rv1573" 1 -"Rv3557c" "Rv2145c" 1 -"Rv3557c" "Rv2452c" 1 -"Rv3557c" "Rv2549c" 1 -"Rv3557c" "Rv2550c" 1 -"Rv3557c" "Rv3549c" 1 -"Rv3557c" "Rv3550" 1 -"Rv3557c" "Rv3560c" 1 -"Rv3557c" "Rv3561" 1 -"Rv3574" "Rv3574" 1 -"Rv3574" "Rv0103c" 1 -"Rv3574" "Rv0104" 1 -"Rv3574" "Rv0139" 1 -"Rv3574" "Rv0157A" 1 -"Rv3574" "Rv0158" 1 -"Rv3574" "Rv0171" 1 -"Rv3574" "Rv0176" 1 -"Rv3574" "Rv0177" 1 -"Rv3574" "Rv0218" 1 -"Rv3574" "Rv0219" 1 -"Rv3574" "Rv0267" 1 -"Rv3574" "Rv0327c" 1 -"Rv3574" "Rv0354c" 1 -"Rv3574" "Rv0456A" 1 -"Rv3574" "Rv0461" 1 -"Rv3574" "Rv0488" 1 -"Rv3574" "Rv0490" 1 -"Rv3574" "Rv0499" 1 -"Rv3574" "Rv0503c" 1 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"Rv1884c" 1 -"Rv3830c" "Rv1886c" 1 -"Rv3830c" "Rv1990c" 1 -"Rv3830c" "Rv2011c" 1 -"Rv3830c" "Rv2012" 1 -"Rv3830c" "Rv2107" 1 -"Rv3830c" "Rv2154c" 1 -"Rv3830c" "Rv2155c" 1 -"Rv3830c" "Rv2293c" 1 -"Rv3830c" "Rv2390c" 1 -"Rv3830c" "Rv2392" 1 -"Rv3830c" "Rv2403c" 1 -"Rv3830c" "Rv2436" 1 -"Rv3830c" "Rv2516c" 1 -"Rv3830c" "Rv2517c" 1 -"Rv3830c" "Rv2708c" 1 -"Rv3830c" "Rv2709" 1 -"Rv3830c" "Rv2712c" 1 -"Rv3830c" "Rv2713" 1 -"Rv3830c" "Rv2816c" 1 -"Rv3830c" "Rv2929" 1 -"Rv3830c" "Rv2946c" 1 -"Rv3830c" "Rv3017c" 1 -"Rv3830c" "Rv3179" 1 -"Rv3830c" "Rv3246c" 1 -"Rv3830c" "Rv3294c" 1 -"Rv3830c" "Rv3487c" 1 -"Rv3830c" "Rv3607c" 1 -"Rv3830c" "Rv3742c" 1 -"Rv3830c" "Rv3746c" 1 -"Rv3830c" "Rv3747" 1 -"Rv3830c" "Rv3809c" 1 -"Rv3830c" "Rv3829c" 1 -"Rv3830c" "Rv3831" 1 -"Rv3830c" "Rv3856c" 1 -"Rv3830c" "Rv3878" 1 -"Rv3833" "Rv3833" 1 -"Rv3833" "Rv3832c" 1 -"Rv3849" "Rv0397" 1 -"Rv3849" "Rv1089A" 1 -"Rv3849" "Rv2143" 1 -"Rv3849" "Rv0010c" 1 -"Rv3849" "Rv0025" 1 -"Rv3849" "Rv0139" 1 -"Rv3849" "Rv0405" 1 -"Rv3849" "Rv0635" 1 -"Rv3849" "Rv0684" 1 -"Rv3849" "Rv0717" 1 -"Rv3849" "Rv0947c" 1 -"Rv3849" "Rv1067c" 1 -"Rv3849" "Rv1297" 1 -"Rv3849" "Rv1306" 1 -"Rv3849" "Rv1356c" 1 -"Rv3849" "Rv1402" 1 -"Rv3849" "Rv1479" 1 -"Rv3849" "Rv1541c" 1 -"Rv3849" "Rv1810" 1 -"Rv3849" "Rv1811" 1 -"Rv3849" "Rv2665" 1 -"Rv3849" "Rv2929" 1 -"Rv3849" "Rv2938" 1 -"Rv3849" "Rv3047c" 1 -"Rv3849" "Rv3239c" 1 -"Rv3849" "Rv3343c" 1 -"Rv3849" "Rv3416" 1 -"Rv3849" "Rv3463" 1 -"Rv3849" "Rv3488" 1 -"Rv3849" "Rv3614c" 1 -"Rv3849" "Rv3890c" 1 -"Rv3849" "Rv3917c" 1 -"Rv3849" "Rv3922c" 1 -"Rv3849" "Rv0033" 1 -"Rv3849" "Rv0172" 1 -"Rv3849" "Rv0386" 1 -"Rv3849" "Rv0873" 1 -"Rv3849" "Rv1364c" 1 -"Rv3849" "Rv1478" 1 -"Rv3849" "Rv1490" 1 -"Rv3849" "Rv1497" 1 -"Rv3849" "Rv1762c" 1 -"Rv3849" "Rv1816" 1 -"Rv3849" "Rv1824" 1 -"Rv3849" "Rv2145c" 1 -"Rv3849" "Rv2237" 1 -"Rv3849" "Rv2307A" 1 -"Rv3849" "Rv2307D" 1 -"Rv3849" "Rv2560" 1 -"Rv3849" "Rv2783c" 1 -"Rv3849" "Rv2957" 1 -"Rv3849" "Rv3020c" 1 -"Rv3849" "Rv3144c" 1 -"Rv3849" "Rv3715c" 1 -"Rv3849" "Rv3781" 1 -"Rv3849" "Rv3812" 1 -"Rv3855" "Rv3855" 1 -"Rv3855" "Rv0456A" 1 -"Rv3855" "Rv1116" 1 -"Rv3855" "Rv1256c" 1 -"Rv3855" "Rv1572c" 1 -"Rv3855" "Rv1573" 1 -"Rv3855" "Rv1665" 1 -"Rv3855" "Rv1963c" 1 -"Rv3855" "Rv1986" 1 -"Rv3855" "Rv2107" 1 -"Rv3855" "Rv2145c" 1 -"Rv3855" "Rv2307B" 1 -"Rv3855" "Rv2452c" 1 -"Rv3855" "Rv2547" 1 -"Rv3855" "Rv2779c" 1 -"Rv3855" "Rv2780" 1 -"Rv3855" "Rv3269" 1 -"Rv3855" "Rv3290c" 1 -"Rv3855" "Rv3746c" 1 -"Rv3855" "Rv3747" 1 -"Rv3855" "Rv3854c" 1 -"Rv3862c" "Rv3872" 1 -"Rv3862c" "Rv3881c" 1 -"Rv3862c" "Rv1870c" 1 -"Rv3862c" "Rv3616c" 1 -"Rv3862c" "Rv3778c" 1 -"Rv3862c" "Rv3779" 1 -"Rv3911" "Rv2515c" 1 -"Rv3911" "Rv3906c" 1 diff --git a/tests/testthat.R b/tests/testthat.R index 0c33a55a..235ea9b2 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -2,7 +2,6 @@ library(testthat) library(netZooR) #download test data -download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/ppi.txt','testthat/ppi.txt') download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/ppi_medium.txt','testthat/ppi_medium.txt') download.file('https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/testDataset.RData','testthat/testDataset.RData') diff --git a/tests/testthat/test-panda.R b/tests/testthat/test-panda.R index f1b39ab2..0096cb2d 100644 --- a/tests/testthat/test-panda.R +++ b/tests/testthat/test-panda.R @@ -7,10 +7,10 @@ test_that("panda function works", { expect_error(pandaPy()) # input file path - system("curl -O https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/expr4.txt") - T4_expression_file_path <- "./expr4.txt" - motif_file_path <- system.file("extdata", "chip.txt", package = "netZooR", mustWork = TRUE) - ppi_file_path <- "./ppi.txt" + system("curl -O https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/expr4_200_L.txt") + T4_expression_file_path <- "./expr4_200_L.txt" + motif_file_path <- system.file("extdata", "chip_medium.txt", package = "netZooR", mustWork = TRUE) + ppi_file_path <- "./ppi_medium.txt" # test 2: check message when only expression data input # To do 1: error occurred when only expression as input dataset @@ -22,19 +22,19 @@ test_that("panda function works", { # test 4: when all arguments are default # computing="cpu", precision="double",save_memory=FALSE, save_tmp=TRUE, keep_expression_matrix=FALSE, modeProcess="union", remove_missing=FALSE test1Panda<- pandaPy(T4_expression_file_path, motif_file_path, ppi_file_path)$panda - expect_equal(test1Panda[1,4],-0.01782158,tolerance=1e-7) + expect_equal(test1Panda[1,4],-0.08132568,tolerance=1e-7) # test 5: check if PANDA result is correct when arguments settiing like below: # i.e computing = "cpu", save_memory =T , precision="single", save_memory = T, save_tmp=F, keep_expression_matrix = T, modeProcess = 'intersection' test2Panda <- pandaPy(T4_expression_file_path, motif_file_path,ppi_file_path,precision = "single", save_memory = T, save_tmp = F,keep_expression_matrix = TRUE, modeProcess = "intersection" )$WAMpanda - expect_equal(test2Panda[1,1],-0.26648718, tolerance=1e-5) + expect_equal(test2Panda[1,1],2.229422, tolerance=1e-5) # test 6: when processMode = legacy, remove_missing=FALSE test3Panda <- pandaPy(T4_expression_file_path, motif_file_path,ppi_file_path, modeProcess = "legacy", remove_missing = FALSE)$panda - expect_equal(test3Panda[1,4],-0.06200149888611282,tolerance=1e-7) + expect_equal(test3Panda[1,4],5.86307,tolerance=1e-7) # test 7: when processMode = legacy, remove_missing=TRUE - test4List <- pandaPy(T4_expression_file_path, motif_file_path,ppi_file_path, modeProcess = "legacy", remove_missing = TRUE) + test4List <- pandaPy(T4_expression_file_path, motif_file_path,ppi_file_path, modeProcess = "legacy", remove_missing = TRUE) test4Panda <- test4List$panda # test 8-11: check data type in PANDA network @@ -44,7 +44,7 @@ test_that("panda function works", { expect_equal(class(test4Panda$Score), "numeric") # test 12: check PANDA network result - expect_equal(test4Panda[1,4],-0.11907165898368743,tolerance=1e-7) + expect_equal(test4Panda[1,4],-0.4123061,tolerance=1e-7) # test 13-15: check if PANDA indegree network is correct @@ -52,14 +52,14 @@ test_that("panda function works", { expect_equal(class(test4Indegree$`Target`), "character") expect_equal(class(test4Indegree$`Target_Score`), "numeric") - expect_equal(test4Indegree[1,2], -10.121892597769255,tolerance=1e-7) + expect_equal(test4Indegree[1,2], 0.1914127,tolerance=1e-7) # test 15-18: check if PANDA outdegree network is correct test4Outdegree <- test4List$outdegree expect_equal(class(test4Outdegree$`Regulator`), "character") expect_equal(class(test4Outdegree$`Regulator_Score`), "numeric") - expect_equal(test4Outdegree[1,2], 87.88068957294422,tolerance=1e-7) + expect_equal(test4Outdegree[1,2], -12.23053,tolerance=1e-6) })