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Update readme - fix logo #24

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Feb 21, 2024
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Update readme - fix logo #24

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a2ccfdd
update readme
wvictor14 Feb 21, 2024
060e15e
logo px
wvictor14 Feb 21, 2024
0d0f775
Increment version number to 1.9.4
wvictor14 Feb 21, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,6 +1,6 @@
Package: planet
Title: Placental DNA methylation analysis tools
Version: 1.9.3
Version: 1.9.4
Authors@R:
c(person("Victor", "Yuan", email = "[email protected]",
role = c("aut", "cre")),
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2 changes: 2 additions & 0 deletions NEWS.md
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# planet 1.9.4

# planet 1.9.3 (09-08-2023)

* add stop controls to `predictEthnicity`
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5 changes: 2 additions & 3 deletions README.Rmd
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Expand Up @@ -16,11 +16,10 @@ knitr::opts_chunk$set(
)
```

# planet <img src="man/figures/logo.png" align="right" height = "139" />
# planet <img src="man/figures/logo.png" align="right" height = "100px" style="float:right; height:100px;"/>

<!-- badges: start -->
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4321633.svg)](https://doi.org/10.5281/zenodo.4321633) `r badger::badge_last_commit("GuangchuangYu/badger")`
[![R build status](https://github.com/wvictor14/planet/workflows/R-CMD-check/badge.svg)](https://github.com/wvictor14/planet/actions)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4321633.svg)](https://doi.org/10.5281/zenodo.4321633) `r badger::badge_last_commit("GuangchuangYu/badger")`
[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
[![R-CMD-check](https://github.com/wvictor14/planet/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/wvictor14/planet/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
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52 changes: 25 additions & 27 deletions README.md
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@@ -1,12 +1,10 @@

# planet <img src="man/figures/logo.png" align="right" height = "139" />
# planet <img src="man/figures/logo.png" align="right" height = "100px" style="float:right; height:100px;"/>

<!-- badges: start -->

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4321633.svg)](https://doi.org/10.5281/zenodo.4321633)
[![](https://img.shields.io/github/last-commit/GuangchuangYu/badger.svg)](https://github.com/GuangchuangYu/badger/commits/main)
[![R build
status](https://github.com/wvictor14/planet/workflows/R-CMD-check/badge.svg)](https://github.com/wvictor14/planet/actions)
[![Lifecycle:
stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
[![R-CMD-check](https://github.com/wvictor14/planet/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/wvictor14/planet/actions/workflows/R-CMD-check.yaml)
Expand Down Expand Up @@ -66,16 +64,16 @@ predictEthnicity(plBetas) %>%
head()
#> 1860 of 1860 predictors present.
#> # A tibble: 6 × 7
#> Sample_ID Predicted_ethnicity_nothresh Predicted_ethnicity
#> <chr> <chr> <chr>
#> 1 GSM1944936 Caucasian Caucasian
#> 2 GSM1944939 Caucasian Caucasian
#> 3 GSM1944942 Caucasian Caucasian
#> 4 GSM1944944 Caucasian Caucasian
#> 5 GSM1944946 Caucasian Caucasian
#> 6 GSM1944948 Caucasian Caucasian
#> # ℹ 4 more variables: Prob_African <dbl>, Prob_Asian <dbl>,
#> # Prob_Caucasian <dbl>, Highest_Prob <dbl>
#> Sample_ID Predicted_ethnicity_n…¹ Predicted_ethnicity Prob_African Prob_Asian
#> <chr> <chr> <chr> <dbl> <dbl>
#> 1 GSM1944936 Caucasian Caucasian 0.00331 0.0164
#> 2 GSM1944939 Caucasian Caucasian 0.000772 0.000514
#> 3 GSM1944942 Caucasian Caucasian 0.000806 0.000699
#> 4 GSM1944944 Caucasian Caucasian 0.000883 0.000792
#> 5 GSM1944946 Caucasian Caucasian 0.000885 0.00130
#> 6 GSM1944948 Caucasian Caucasian 0.000852 0.000973
#> # ℹ abbreviated name: ¹​Predicted_ethnicity_nothresh
#> # ℹ 2 more variables: Prob_Caucasian <dbl>, Highest_Prob <dbl>
```

#### Predict Gestational Age
Expand Down Expand Up @@ -112,20 +110,20 @@ minfi:::projectCellType(
lessThanOne = FALSE) %>%

head()
#> Trophoblasts Stromal Hofbauer Endothelial
#> GSM1944936 0.1091279 0.04891919 0.000000e+00 0.08983998
#> GSM1944939 0.2299918 0.00000000 -1.806592e-19 0.07888007
#> GSM1944942 0.1934287 0.03483540 0.000000e+00 0.09260353
#> GSM1944944 0.2239896 0.06249135 1.608645e-03 0.11040693
#> GSM1944946 0.1894152 0.07935955 0.000000e+00 0.10587439
#> GSM1944948 0.2045124 0.07657717 0.000000e+00 0.09871149
#> nRBC Syncytiotrophoblast
#> GSM1944936 0.05294062 0.6979477
#> GSM1944939 0.03374149 0.6377822
#> GSM1944942 0.02929310 0.6350506
#> GSM1944944 0.04447951 0.5467642
#> GSM1944946 0.05407587 0.6022329
#> GSM1944948 0.02269798 0.6085825
#> Trophoblasts Stromal Hofbauer Endothelial nRBC
#> GSM1944936 0.1091279 0.04891919 0.000000e+00 0.08983998 0.05294062
#> GSM1944939 0.2299918 0.00000000 -1.806592e-19 0.07888007 0.03374149
#> GSM1944942 0.1934287 0.03483540 0.000000e+00 0.09260353 0.02929310
#> GSM1944944 0.2239896 0.06249135 1.608645e-03 0.11040693 0.04447951
#> GSM1944946 0.1894152 0.07935955 0.000000e+00 0.10587439 0.05407587
#> GSM1944948 0.2045124 0.07657717 0.000000e+00 0.09871149 0.02269798
#> Syncytiotrophoblast
#> GSM1944936 0.6979477
#> GSM1944939 0.6377822
#> GSM1944942 0.6350506
#> GSM1944944 0.5467642
#> GSM1944946 0.6022329
#> GSM1944948 0.6085825
```

### References
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