# QC Report

#### gimap (v0.1.0)

#### 2024-07-29

# Unfiltered/raw data

## Counts CDF

## Histogram of cpm values by sample

## Sample Correlation heatmap (unfiltered data)

## Variance within replicates

## Plasmid expression (log 2 cpm values for Day 0 sample/time point)

# Applying potential filters

## Filter pgRNAs where there is a count of 0 for any sample/time point

### Replicates with a pgRNA count of 0

If this filter is applied, this is the number of pgRNAs that would be filtered out

RawCount0 | n | percent
--- | --- | ---
FALSE | 31977 | 96.4
TRUE | 1193 | 3.6

### Filter pgRNAs where there is a low log2 CPM value for the plasmid sample/time point

If this filter is applied, this is the number of pgRNAs that would be filtered out

Plasmid_log2cpmBelowCutoff | n | percent
--- | --- | ---
FALSE | 32873 | 99.1
TRUE | 297 | 0.9

### If both filters are applied

Which Filter(s) | Number of pgRNAs flagged for removal | Percent of total pgRNA constructs
--- | --- | ---
Zero count, but not low plasmid CPM | 1056 | 3.18
Low plasmid CPM, but not zero count | 160 | 0.48
Either Zero count or Low plasmid CPM or both | 1353 | 4.08
Both Zero count and Low plasmid CPM | 137 | 0.41
Remaining pgRNAs flagged by no filters | 31817 | 95.92

# Session Info

    ## R version 4.4.0 (2024-04-24)
    ## Platform: x86_64-apple-darwin20
    ## Running under: macOS Ventura 13.5.2
    ##
    ## Matrix products: default
    ## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
    ## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
    ##
    ## locale:
    ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    ##
    ## time zone: America/New_York
    ## tzcode source: internal
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] purrr_1.0.2   ggplot2_3.5.1 dplyr_1.1.4   gimap_0.1.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] sass_0.4.9         utf8_1.2.4         generics_0.1.3     tidyr_1.3.1
    ##  [5] xml2_1.3.6         stringi_1.8.4      hms_1.1.3          digest_0.6.36
    ##  [9] magrittr_2.0.3     evaluate_0.24.0    grid_4.4.0         timechange_0.3.0
    ## [13] RColorBrewer_1.1-3 fastmap_1.2.0      jsonlite_1.8.8     fansi_1.0.6
    ## [17] viridisLite_0.4.2  scales_1.3.0       jquerylib_0.1.4    cli_3.6.3
    ## [21] rlang_1.1.4        crayon_1.5.3       bit64_4.0.5        munsell_0.5.1
    ## [25] cachem_1.1.0       withr_3.0.0        yaml_2.3.10        tools_4.4.0
    ## [29] parallel_4.4.0     tzdb_0.4.0         colorspace_2.1-1   kableExtra_1.4.0
    ## [33] vctrs_0.6.5        R6_2.5.1           lifecycle_1.0.4    lubridate_1.9.3
    ## [37] snakecase_0.11.1   stringr_1.5.1      bit_4.0.5          vroom_1.6.5
    ## [41] janitor_2.2.0      pkgconfig_2.0.3    bslib_0.7.0.9000   pillar_1.9.0
    ## [45] gtable_0.3.5       glue_1.7.0         systemfonts_1.1.0  highr_0.11
    ## [49] xfun_0.46          tibble_3.2.1       tidyselect_1.2.1   rstudioapi_0.16.0
    ## [53] knitr_1.48         farver_2.1.2       htmltools_0.5.8.1  labeling_0.4.3
    ## [57] rmarkdown_2.27     svglite_2.1.3      readr_2.1.5        pheatmap_1.0.12
    ## [61] compiler_4.4.0