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# Intro to Computing

*Slides that go with this lesson can be found [here](slides/lesson1_slides.html).*

## Goals of the course

- Fundamental concepts in high-level programming languages (R, Python, Julia, WDL, etc.) that is transferable: *How do programs run, and how do we solve problems using functions and data structures?*
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```

```r
length("ATCG")
nchar("ATCG")
```

```
## [1] 1
## [1] 4
```

Here, our input **data types** to the operation are **numeric** in lines 1-4 and our input data type to the function is **character** in line 5.
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Lastly, a note on the use of functions: a programmer should not need to know how the function is implemented in order to use it - this emphasizes [abstraction and modular thinking](#a-programming-language-has-following-elements), a foundation in any programming language.


### Data types

Here are some data types that we will be using in this course:

- **Numeric**: 18, 21, 65, 1.25

- **Character**: "ATCG", "Whatever", "948-293-0000"

- **Logical**: TRUE, FALSE


## Grammar Structure 2: Storing data types in the global environment

To build up a computer program, we need to store our returned data type from our expression somewhere for downstream use. We can assign a variable to it as follows:
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## [1] 18
```

## Functions to read in data

We are going to read in a Comma Separated Value (CSV) spreadsheet, that contains information about cancer cell lines.

The first line calls the function `read.csv()` with a string argument representing the file path to the CSV file (we are using an URL online, but this is typically done locally), and the returned data type is stored in `metadata` variable. The resulting `metadata` variable is a new data type you have never seen before. It is a **data structure** called a **data frame** that we will be exploring next week. It holds a table of several data types that we can explore.

We run a few functions on `metadata`.


```r
metadata = read.csv("https://github.com/caalo/Intro_to_R/raw/main/classroom_data/CCLE_metadata.csv")
head(metadata)
```

```
## ModelID PatientID CellLineName StrippedCellLineName Age SourceType
## 1 ACH-000001 PT-gj46wT NIH:OVCAR-3 NIHOVCAR3 60 Commercial
## 2 ACH-000002 PT-5qa3uk HL-60 HL60 36 Commercial
## 3 ACH-000003 PT-puKIyc CACO2 CACO2 72 Commercial
## 4 ACH-000004 PT-q4K2cp HEL HEL 30 Commercial
## 5 ACH-000005 PT-q4K2cp HEL 92.1.7 HEL9217 30 Commercial
## 6 ACH-000006 PT-ej13Dz MONO-MAC-6 MONOMAC6 64 Commercial
## SangerModelID RRID DepmapModelType AgeCategory GrowthPattern
## 1 SIDM00105 CVCL_0465 HGSOC Adult Adherent
## 2 SIDM00829 CVCL_0002 AML Adult Suspension
## 3 SIDM00891 CVCL_0025 COAD Adult Adherent
## 4 SIDM00594 CVCL_0001 AML Adult Suspension
## 5 SIDM00593 CVCL_2481 AML Adult Mixed
## 6 SIDM01023 CVCL_1426 AMOL Adult Suspension
## LegacyMolecularSubtype PrimaryOrMetastasis SampleCollectionSite
## 1 Metastatic ascites
## 2 Primary haematopoietic_and_lymphoid_tissue
## 3 Primary Colon
## 4 Primary haematopoietic_and_lymphoid_tissue
## 5 bone_marrow
## 6 Primary haematopoietic_and_lymphoid_tissue
## Sex SourceDetail LegacySubSubtype CatalogNumber
## 1 Female ATCC high_grade_serous HTB-71
## 2 Female ATCC M3 CCL-240
## 3 Male ATCC HTB-37
## 4 Male DSMZ M6 ACC 11
## 5 Male ATCC M6 HEL9217
## 6 Male DSMZ M5 ACC 124
## CCLEName COSMICID PublicComments
## 1 NIHOVCAR3_OVARY 905933
## 2 HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE 905938
## 3 CACO2_LARGE_INTESTINE NA
## 4 HEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE 907053
## 5 HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE NA
## 6 MONOMAC6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE 908148
## WTSIMasterCellID EngineeredModel TreatmentStatus OnboardedMedia PlateCoating
## 1 2201 MF-001-041 None
## 2 55 MF-005-001 None
## 3 NA Unknown MF-015-009 None
## 4 783 Post-treatment MF-001-001 None
## 5 NA MF-001-001 None
## 6 2167 MF-001-001 None
## OncotreeCode OncotreeSubtype OncotreePrimaryDisease
## 1 HGSOC High-Grade Serous Ovarian Cancer Ovarian Epithelial Tumor
## 2 AML Acute Myeloid Leukemia Acute Myeloid Leukemia
## 3 COAD Colon Adenocarcinoma Colorectal Adenocarcinoma
## 4 AML Acute Myeloid Leukemia Acute Myeloid Leukemia
## 5 AML Acute Myeloid Leukemia Acute Myeloid Leukemia
## 6 AMOL Acute Monoblastic/Monocytic Leukemia Acute Myeloid Leukemia
## OncotreeLineage
## 1 Ovary/Fallopian Tube
## 2 Myeloid
## 3 Bowel
## 4 Myeloid
## 5 Myeloid
## 6 Myeloid
```

```r
nrow(metadata)
```

```
## [1] 1864
```

```r
ncol(metadata)
```

```
## [1] 30
```

If you don't know what a function does, ask for help:


```r
?nrow
```

## Tips on Exercises / Debugging

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